Alapaha MFL Final

TECHNICAL REPORT
MFL Establishment
for the
Alapaha River
March 2008
Water Resource Associates, Inc.

Engineering ~ Planning ~ Environmental Science
4260 West Linebaugh Ave, Tampa, FL 3362
Phone: 813-265-3130
Fax: 813-265-6610
www.wraconsultants.com
In association with:
SDII Global Janicki Environmental

TABLE OF CONTENTS
List of Figures .............................................................................................................................. iv
List of Tables................................................................................................................................ xi
Executive Summary .....................................................................................................................xii
1.0 INTRODUCTION....................................................................................................1-1
1.1 State of Florida Law Pertaining to the Establishment of MFLS ..............................1-1
1.2 Project Scope .........................................................................................................1-2
1.3 Water Body Regulatory Designations ....................................................................1-2
1.4 Relevant Environmental and Water Resource Values ...........................................1-4
1.4.1 Method of Identification of Relevant Environmental and
Water Resource Values .........................................................................................1-4
1.4.2 Application of the EWRV Review Process .............................................................1-7
2.0 INTRODUCTION TO THE SUWANNEE RIVER BASIN AND STUDY AREA ......2-1
2.1 Suwannee River Basin ...........................................................................................2-1
2.1.1 Physical Setting of the Suwannee Basin................................................................2-1
2.1.2 Climate of the Suwannee River Basin....................................................................2-6
2.1.3 Geology of the Suwannee River Basin.................................................................2-10
2.1.4 Regional Aquifer Systems ....................................................................................2-13
2.1.5 Land and Water Use in the Suwannee River Basin .............................................2-18
2.1.5.1 Land Use and Population Characteristics ............................................................2-18
2.1.5.2 Water Use ............................................................................................................2-20
2.2 Suwannee River ...................................................................................................2-22
2.2.1 Surfacewater Hydrology .......................................................................................2-22
2.2.1.1 Annual Yield .........................................................................................................2-22
2.2.1.2 Spatial Flow Patterns ...........................................................................................2-24
2.2.1.3 Seasonal Flow Patterns .......................................................................................2-26
2.2.1.4 Tidal River and Estuary ........................................................................................2-28
2.2.1.5 Chemical Characteristics......................................................................................2-31
2.2.2 Ecology.................................................................................................................2-34
2.2.2.1 Aquatic and Wetland Communities ......................................................................2-34
2.2.2.2 River Reach Ecology............................................................................................2-34
2.2.2.2.1 Suwannee River Mainstem ..................................................................................2-34
2.2.2.2.2 Santa Fe River .....................................................................................................2-37
2.2.2.2.3 Withlacoochee River ............................................................................................2-38
2.2.2.2.4 Alapaha River.......................................................................................................2-38
2.2.2.2.5 Suwannee Estuary ...............................................................................................2-39
2.2.2.2.6 Species and Habitats of Interest ........................................................................2-39
2.3 Alapaha River Drainage Basin and Related Springs............................................2-45
2.3.1 Introduction...........................................................................................................2-45
i
2.3.2 Population and Water Use ...................................................................................2-48
2.3.2.1 Population Distribution .........................................................................................2-48
2.3.2.2 Land Use ..............................................................................................................2-50
2.3.2.3 Water Use ............................................................................................................2-51
2.3.3 Topography, Physiography, and Drainage...........................................................2-51
2.3.4 Geology and Hydrology........................................................................................2-56
2.3.4.1 Local Stratigraphy and Geomorphology...............................................................2-56
2.3.4.2 Surfacewater Hydrology .......................................................................................2-58
2.3.4.3 Karst and Groundwater Hydrology .......................................................................2-58
3.0 HYDROLOGIC ANALYSES ..................................................................................3-1

3.1 Overview ................................................................................................................3-1
3.2 Data Availability......................................................................................................3-1
3.2.1. Groundwater Data ..................................................................................................3-1
3.2.1.1 Groundwater Levels ...............................................................................................3-1
3.2.1.2 Groundwater Quality ..............................................................................................3-3
3.2.2 Surfacewater Data..................................................................................................3-3
3.2.3 Precipitation Data ..................................................................................................3-3
3.2.4 Permit Data ...........................................................................................................3-6
3.2.5 Summary ...............................................................................................................3-6
3.3 Data Simulation and Analysis.................................................................................3-6
3.3.1 Methods..................................................................................................................3-6
3.3.1.1 Simulation of River Data.........................................................................................3-6
3.3.1.2 Simulation of Alapaha Rise Discharge ...................................................................3-7
3.3.1.3 Uncertainty Associated With Data Simulation ........................................................3-8
3.3.2 Alapaha River.........................................................................................................3-8
3.3.2.1 Alapaha River at Statenville ...................................................................................3-8
3.3.2.2 Alapaha River near Jennings ..............................................................................3-11
3.3.2.3 Alapaha River near Jasper...................................................................................3-15
3.3.2.4 Summary of River Data Simulation ......................................................................3-19
3.3.3 Predicting Resurgence Discharge........................................................................3-19
3.3.3.1 Alapaha Rise ........................................................................................................3-19
3.3.3.2 Holton Creek Rise ................................................................................................3-37
3.3.4 Discussion ..........................................................................................................3-37
3.4 HEC-RAS Model for the Alapaha River................................................................3-43
3.4.1 Model Data Development.....................................................................................3-44
3.4.1.1 Model Boundary conditions ..................................................................................3-44
3.4.1.2 Model Calibration data .........................................................................................3-45
3.4.2 HEC-RAS Model Development ............................................................................3-45
3.4.2.1 HEC-RAS Model Calibration ................................................................................3-49
3.4.2.2 Exported HEC-RAS Data for EFM .......................................................................3-52
ii
3.5 Use of the Discharge Data for MFL Development................................................3-53
3.6 Temporal Variability of Hydrologic Conditions in the
Alapaha River ......................................................................................................3-54
4.0 ECOLOGICAL ANALYSES ..................................................................................4-1

4.1 General Description ...............................................................................................4-1
4.1.1 Physical Setting......................................................................................................4-1
4.1.2 Riparian Area .........................................................................................................4-3
4.2 Water Quality..........................................................................................................4-7
4.3 Benthos ..................................................................................................................4-9
4.4 Mussels ................................................................................................................4-14
4.5 Fish.......................................................................................................................4-16
4.5.1 Groups of Fish Present in the Suwannee Drainage .............................................4-18
4.6 Summary ..............................................................................................................4-23
5.0 ECOLOGICAL BASIS FOR A MINIMUM FLOW FOR THE ALAPAHA RIVER ...5-1
5.1 Methods ..................................................................................................................5-1
5.1.1 Wetted Perimeter ...................................................................................................5-1
5.1.2 Instream Flow Methods...........................................................................................5-6
5.1.2.1 Ecosystem Functions Model .................................................................................5-6
5.1.3 Fish Passage........................................................................................................5-10
5.2 Results ................................................................................................................5-11
5.2.1 Wetted Perimeter Results ....................................................................................5-11
5.2.2 EFM Results.........................................................................................................5-12
5.2.3 Minimum Fish Passage Results ...........................................................................5-13
5.3 Recommended MFLs ...........................................................................................5-16
6.0 SUMMARY AND MFL RECOMMENDATIONS .....................................................6-1

6.1 Alapaha River Study Area ......................................................................................6-1
6.2 MFL Evaluation Procedure.....................................................................................6-1
6.3 MFL Evaluation Summary ......................................................................................6-2
6.4 Recommended MFLs .............................................................................................6-3
6.4.1 Proposed MFL for the Alapaha River at Jennings..................................................6-3
APPENDICES:
Appendix 4-A Additional Water Quality Plots Alapaha River
Appendix 4-B List of Fish Species Reported in the Suwannee Drainage Compiled from
Hellier (1967) and Bass (1991)
LITERATURE CITED
iii
List of Figures
Figure 1-1a. Total extent of the Alapaha drainage basin. .......................................................1-3

Figure 1-1b Extent of the Alapaha River Basin in Hamilton
County, Florida. ..................................................................................................1-4
Figure 1-2 Flow chart illustrating the method used to identify
the Environmental and Water Resource Values (EWRV)
that are limiting for MFL development on a water body......................................1-5
Figure 2-1 Suwannee River Basin in Florida and Georgia.

Basins shown are USGS hydrologic units ..........................................................2-2
Figure 2-2 Physiographic regions in the SRWMD and regional
hydrography in relation to the Suwannee River Basin in Florida........................2-3
Figure 2-3 Marine terraces in the SRWMD in relation to the
Suwannee River Basin .......................................................................................2-5
Figure 2-4 Average annual and monthly rainfall patterns in
the Suwannee River Basin .................................................................................2-7
Figure 2-5 Twelve-month total rainfall for the North Florida
climate division for the period 1900 to 2003.
Rainfall totals are running averages, and are plotted
at the first month of the 12-month period............................................................2-8
Figure 2-6 Mean monthly rainfall and reference evapotranspiration
in the north Florida region. ................................................................................2-9
Figure 2-7 Extent of the limestone unit bearing the Floridan
aquifer system in the southeastern U.S.
Fault line labels indicate: U = Uplift; D = Downlift............................................2-11
Figure 2-8 Elevation of the upper surface of the Tertiary
limestone strata that constitute the Floridan
aquifer within the District. .................................................................................2-12
Figure 2-9 Generalized geologic cross section of the region.............................................2-14
Figure 2-10 Potentiometric surface of the Floridan aquifer in
May 1976..........................................................................................................2-16
Figure 2-11 Confinement conditions of the Floridan aquifer system
in the region......................................................................................................2-17
Figure 2-12 Map showing permitted water use patterns in the
SRWMD. Each symbol represents the sum of the
Average Daily Rate of Withdrawal (ADR) within
each 1 mi.2 section. ..........................................................................................2-21
Figure 2-13 Daily and annual discharge (1942-2003) for the
Suwannee River near Wilcox (USGS Station Number 02323500)...................2-23
Figure 2-14 Daily and annual discharge (1942-2003) for the
Suwannee River near Wilcox (USGS Station Number 02323500)...................2-23
Figure 2-15 Relationship between annual rainfall and discharge
for the Suwannee River near Wilcox
(USGS Station Number 02323500). .................................................................2-24
Figure 2-16 Relationship of drainage area and mean annual
discharge for the Suwannee Basin for gages with
10 or more years of systematic record. ............................................................2-25
iv
Figure 2-17 Mean monthly discharge at four USGS gaging sites
on the upper (A) and lower (B) Suwannee and
Santa Fe Rivers, reflecting stream hydrology in the upper
and lower portions of the drainage. ..................................................................2-26
Figure 2-18 Climatic river-basin divide of Heath and
Conover (1981) River pattern data from Kelly (2004).......................................2-27
Figure 2-19 Gage locations and mean monthly discharge
patterns at selected long term surfacewater gages in the
Suwannee River Basin. Discharge expressed as a
proportion of mean annual discharge at each gage. ........................................2-29
Figure 2-20 Major features of the Suwannee estuary..........................................................2-30
Figure 2-21 Map showing the ecological reaches of the
Suwannee River in Florida ...............................................................................2-32
Figure 2-22 Plot of mean alkalinity (mg/L as CaCO3) in the five
reaches of the Suwannee River in Florida........................................................2-33
Figure 2-23 Plot of mean color (platinum cobalt units; PCU) in the
five reaches of the Suwannee River in Florida .................................................2-33
Figure 2-24 Basic geomorphology of the river channel and
floodplain and typical plant communities in each of the
five ecological reaches (Figure 2-20) of the Suwannee River ..........................2-35
Figure 2-25 Rock-bound channel at shoals area north of the
CR 150 Bridge (Figure 1-1b. Note the emergent
sand bar at left center of image ........................................................................2-45
Figure 2-26 Rock shoals approximately 1 mile upstream of the
CR 150 bridge over the Alapaha River.
(Bridge is located at Sasser Landing, near
Jennings, Florida Figure 1-1b.)......................................................................2-45
Figure 2-27 View of the Alapaha River looking north
(upstream from the CR 150 bridge at Sasser Landing Figure 1-1b).
River is at low flood stage ................................................................................2-45
Figure 2-28 Sinkhole in the bed of the Alapaha River near the
mouth of the Dead River blind valley.
Geologists are standing at the opening of the sinkhole....................................2-45
Figure 2-29 View into the sinkhole shown in Figure 2-28.
The exposed rock consists of limestone and
dolostone of the Statenville Formation
(Miocene Hawthorn Group). .............................................................................2-46
Figure 2-30 Dead River during a drought. In karst terminology,
this is known as a blind valley, a valley that transports
water to a sinkhole, into which the stream disappears. ....................................2-46
Figure 2-31 Dead River sink. Note the rock exposed around the
sinkhole and the drift wood transported to the sink
from the Alapaha River during higher flow conditions. .....................................2-46
Figure 2-32 View looking downstream in the dry Alapaha River
bed at the mouth of the Dead River blind valley...............................................2-47
Figure 2-33 View of the dry Alapaha River bed downstream of the
SR 6 Bridge (Figure 1-1b) and within the reach of the
river where sinkholes capture discharge ..........................................................2-47
Figure 2-34 Mouth of the Alapaha River as seen from the
Suwannee at moderate low flow. Note the
sandy bed incised in limestone bedrock...........................................................2-47
v
Figure 2-35 The Alapaha Rise on the north bank of the Suwannee River.
This normally brown-water spring discharges part of the
water recharged to the Floridan aquifer at the sinkholes
upstream on the Alapaha (Figs. 2-28 through 2-31).........................................2-47
Figure 2-36 Holton Spring and the head of Holton Creek....................................................2-48
Figure 2-37 Potentiometric surface of the Floridan aquifer and
approximate location of the Alapaha groundwater
basin in the vicinity of the Alapaha River in Florida ..........................................2-49
Figure 2-38 Major land uses in the Alapaha River Basin of Florida.....................................2-50
Figure 2-39 Topography of the Alapaha River Basin...........................................................2-52
Figure 2-40 Physiographic regions in the Alapaha River Basin of Florida...........................2-54
Figure 2-41 Closed depressions (sinkholes and other karst features)
in the Alapaha River Basin in Florida (study area). .........................................2-55
Figure 2-42 Geologic map of the Alapaha River Basin........................................................2-57
Figure 2-43 Recharge potential in the Alapaha River Basin. ...............................................2-60
Figure 3-1 Location of monitoring wells in the Alapaha River Basin of Florida....................3-2
Figure 3-2 Locations of stream gages in the Alapaha River Basin. .....................................3-4
Figure 3-3 Locations of rainfall stations in the Alapaha River study area ............................3-5
Figure 3-4 Rating curve for the Alapaha River at Statenville, Georgia ................................3-9
Figure 3-5 Comparison of simulated and measured daily stage
of the Alapaha River at Statenville for 1997 through 2003.
Inset compares the simulated and measured values to a 1:1 ratio line............3-10
Figure 3-6 Cross-plot of the stage of the Alapaha River at
Statenville versus daily stage measurements at the
Jennings gage. .................................................................................................3-11
Figure 3-7 Comparison of simulated and measured daily stage
values for the Alapaha River at the gage near Jennings
for the period from 1999 to 2003. Inset compares the
measured and simulated stage data to a 1:1 ratio line.....................................3-12
Figure 3-8 Rating curve based on stage and discharge measurements
at the Jennings gage. .......................................................................................3-13
Figure 3-9 Comparison of simulated and measured daily
discharge from 1999 through 2003 for the Alapaha River
at the gage near Jennings. Inset compares the measured
and simulated data to a 1:1 ratio line................................................................3-14
Figure 3-10 Cross-plot of simulated Alapaha River discharge near
Jennings versus measured discharge of the Alapaha
near Jasper. .....................................................................................................3-16
Figure 3-11 Cross-plot of discharge data from the Alapaha River at
Jennings and Jasper. The graph excludes data when flow at
Jasper was zero and when it was greater than 8,000 cfs.................................3-17
Figure 3-12 Comparison of simulated daily discharge to measured
discharge of the Alapaha River at the gage near Jasper.
Insert compares measured and simulated discharge
to a 1:1 ratio line...............................................................................................3-18
Figure 3-13 Cross-plot of Alapaha Rise discharge measurements
and simulated daily discharge of the Alapaha River near Jennings. ................3-20
Figure 3-14 Cross-plot of discharge measurements from the
Alapaha Rise with simulated daily discharge of the
Alapaha River near Jennings, when river discharge is <500 cfs......................3-22
vi
and simulated, daily Alapaha River discharge near
Jennings for days when Jennings discharge was >500 cfs..............................3-23
Figure 3-16 Cross-correlation graph showing correlations of
Alapaha Rise discharge measurements lagged against
simulated discharge of the Alapaha River at Jennings.
Comparison is for times when Jennings discharge was
less than 500 cfs only.......................................................................................3-24
versus discharge <500 cfs of the Alapaha River near
Jennings lagged 6 days....................................................................................3-25
Figure 3-18 Cross-correlation graph comparing discharge
measurements in the Alapaha Rise to simulated
discharge >500 cfs in the Alapaha River near Jennings.
The arrow indicates the highest correlation at a lag of 21 days .......................3-26
and -21-day lagged discharge >500 cfs in the
Alapaha River near Jennings. ..........................................................................3-27
Figure 3-20 Cross-correlation graph comparing Alapaha Rise
discharge measurements and water levels in Well #10.
Arrow indicates the lag with the highest correlation coefficient. .......................3-29
Figure 3-21 Cross-plot of Alapaha Rise discharge with water levels in
Well #10 lagged 2 days ahead of discharge from the
resurgence (lag = -2 days). ..............................................................................3-31
Figure 3-22 Comparison of daily discharge from the Alapaha Rise
as simulated from lagged water levels in Well #10 with
measured resurgence discharge. .....................................................................3-32
Figure 3-23 Cross-plot of Suwannee River stage at the Ellaville gage
with simulated Alapaha Rise discharge............................................................3-33
Figure 3-24 Cross-plot of stage of the Suwannee River at Ellaville
versus simulated discharge from the Alapaha Rise for
February and March, 1986. The arrows indicate the
direction of time, and the circled data point corresponds
to the peak flow into the swallets in the Alapaha River ....................................3-36
Figure 3-25 Comparison of measured discharge from Holton Rise and Creek
to simulated discharge from the Alapaha Rise ................................................3-38
Figure 3-26 Historic flow duration curve of the Alapaha River near Jennings.
Abrupt offsets in the curve are a result of the data
simulation process............................................................................................3-39
Figure 3-27 Comparison of the flow duration curves for the Alapaha River
at Jasper and at Jennings. The FDC for the flow into the
swallets is shown as part of the Jennings FDC. ...............................................3-40
Figure 3-28 Comparison of the FDCs for flow to the swallets in the
Alapaha River and the Alapaha Rise. Abrupt offsets in the
FDCs are a result of the simulation process.....................................................3-42
Figure 3-29 Model domain, simulated river cross sections, and
observed gage locations. .................................................................................3-43
Figure 3-30 Stage and flows at the Nobles Ferry gage .......................................................3-45
Figure 3-31 River layout showing interpolated cross-sections.............................................3-46
Figure 3-32 River profile with added shoals highlighted ......................................................3-47
vii
Figure 3-33 Shoal at RM 18.44 with elevation 3 above new shoal cross sections
at RM 18.5 and RM 18.48 ................................................................................3-48
Figure 3-34 Calibration at Alapaha River near Jennings (Flow Boundary condition) ..........3-51
Figure 3-35 Calibration at Alapaha River Near Jasper ........................................................3-52
Figure 3-36 Water level profile at low stage ................................................................................ 3-53
Figure 3-37 Box and whisker diagrams showing the monthly variations in stage (A)
and discharge (B) at the Statenville gage ........................................................3-55
Figure 3-38 Box and whisker diagrams showing the monthly variations in stage (A)
and discharge (B) at the Jennings gage on the Alapaha River ........................3-56
Figure 3-39 Box and whisker diagram showing the monthly variations in discharge
at the Jasper gage on the Alapaha River .........................................................3-57
Figure 3-40 Box and whisker diagram showing the monthly variations in simulated
discharge at the Alapaha Rise .........................................................................3-57
Figure 4-1 Locator map of the Alapaha River in Florida showing

major roadways, Alapaha and Holton Creek rises, and the
river mile system ...............................................................................................4-2
Figure 4-2 Map showing the National Wetlands Inventory habitat
categories within the 10-year floodplain on the
Alapaha River in Florida. ....................................................................................4-4
Figure 4-3 Map showing relevant vegetation categories as provided
by the Suwannee River Water Management Districts land use
coverage within the 10 year floodplain on the
Alapaha River of Florida. ....................................................................................4-5
Figure 4-4 Map showing the National Wetlands Inventory water regime
categories within the 10 year floodplain on the
Alapaha River of Florida. ....................................................................................4-6
Figure 4-5 Locator map of the Alapaha River, showing the main
water quality and biology station (ALA010), and a
supplementary biology station (ALA020), maintained by the
Suwannee River Water Management District.....................................................4-7
Figure 4- 6 Mean annual dissolved oxygen (mg/l), with 95%
confidence limits, for the Alapaha River in the
Suwannee River Water Management District.....................................................4-8
Figure 4-7 The relationship between dissolved oxygen at
Suwannee River Water Management District station
ALA010C1 and flow between 1989-2003 ...........................................................4-9
Figure 4-8 Mean annual benthic invertebrate species richness, with
95% confidence limits, for the Alapaha River in the
Suwannee River Water Management District...................................................4-10
Figure 4-9 Mean annual number of benthic invertebrate genera, with
95% confidence limits, for the Alapaha River in the
Figure 4-10 Mean annual benthic invertebrate diversity
(expressed using the Shannon-Weaver Diversity Index),
with 95% confidence limits, for the Alapaha River in the
Figure 4-11 Mean annual measure of eveness (using Pielous Eveness Index),
with 95% confidence limits, for the Alapaha River in the
viii
Figure 4-12 Stacked bar chart showing invertebrate species
richness as distributed throughout the major taxonomic
groups in the Alapaha River. ............................................................................4-13
Figure 4-13 Stacked bar chart showing invertebrate percent
abundance, by major taxonomic group, in the Alapaha River. .........................4-13
Figure 4-14 Historical and current distribution of Quincuncina (=Quadrula)
kleiniana within the Suwannee River drainage,
Florida. = historical site only; = both historical and
recent sites; = recent site only......................................................................4-15
Figure 4-15 Quadrula kleiniana, Suwannee Pigtoe .............................................................4-15
Figure 4-16 Drawings of several members of the sunfish family:
Lepomis aurtus (Redbreast sunfish), Lempomis macrochirus
(Bluegill), Lepomis gulosus (Warmouth) and Lepomis
punctatus (Spotted sunfish)..............................................................................4-18
Figure 4-17 Photographs of two species of Cyprinids,
Notemingonus crysoleucas (Golden shiner) and
Notropis hypselopterus (Sailfin shiner).............................................................4-19
Figure 4-18 Photographs of two representative species of Fundulids,
Fundulus seminolis (Seminole killifish) and Fundulus
lineolatus (line top minnow). .............................................................................4-20
Figure 4-19 Photographs of two darter species in the
Suwannee drainage, Etheostoma edwini (brown darter)
and Percina nigrofasciata (blackbanded darter ...............................................4-21
Figure 4-20 Drawing of Micropterus notius (Suwannee Bass) and its
prey species, the crayfish Procambrus spiculifer. ............................................4-22
Figure 5-1 Examples of a stream cross-section (top) and the

relationship between stream flow and wetted perimeter. ...................................5-2
Figure 5-2 Location of HEC-RAS transects in the Alapaha River in Florida. .......................5-3
Figure 5-3 Bivariate plot of HEC-RAS modeled velocities vs. river mile in the
Alapaha River. The reference line located at river mile
18 shows more variable and higher velocities above this
point on the river and lower velocities below ......................................................5-4
Figure 5-4 Map of HEC-RAS transects in the Alapaha River in
Florida selected for wetted perimeter estimates.................................................5-5
Figure 5-5 Flow-duration curve for the Alapaha River
at the USGS Gage at Jennings (02317620 ........................................................5-9
Figure 5-6 Plots of wetted perimeter vs. flow at river miles
19.3 and 19.93 in the Alapaha River ................................................................5-12
Figure 5-7 Summary of Ecosystem Function Model results for the
Alapaha River protective of a 2.0-foot water depth and a stream
velocity of 0.5 feet sec-1 at the 80th percent exceedance
Suwannee River stage .....................................................................................5-13
Figure 5-8 Fish passage (% of shoal habitat with a minimum depth
greater than 0.6 feet) as a function of flow in the upper
Alapaha River...................................................................................................5-15
Figure 5-9 Flow duration curves representing historic conditions and the
proposed MFL flow duration curve, with reference lines shown at
800 cfs (mid-range flows) and 115 cfs (low flow). ............................................5-17
ix
Figure 6-1 Comparison of Baseline and proposed MFL flow
duration curves for the Alapaha River flow at the Jennings gage ......................6-4
x
List of Tables
Table 1-1 MFL Decision Matrix: Alapaha River .................................................................1-9
Table 2-1 Descriptive data on the Suwannee

River and its major sub-basins ..........................................................................2-1
Table 2-2. Generalized lithostratigraphic column and
aquifer systems in the Suwannee River Basin .................................................2-10
Table 2-3 Land use/land cover conditions in the Florida
portion of the Suwannee River basin, based on 1994
NAPP aerial photography .................................................................................2-19
Table 2-4 Summary of current and projected water use in SRWMD................................2-20
Table 2-5 Discharge Statistics of the Suwannee River at
Wilcox (USGS Station Number 02323500) ......................................................2-22
Table 2-6. Summary of hydrologic characteristics at flow
gaging sites along the Suwannee River and its
major tributaries................................................................................................2-25
Table 2-7 Aquatic and wetland-dependent species of interest
in the lower Suwannee River study area ..........................................................2-40
Table 2-8 FWRI "Selected Taxa" and NOAA "Estuarine Living
Marine Resources" (ELMR) taxa found in the Suwannee estuary ...................2-43
Table 2-9. Aquatic and wetland habitats of conservation interest in the lower
Suwannee study area.......................................................................................2-44
Table 2-10 Estimated Historic and Projected Water
Use (mgd) in Hamilton County, Florida ............................................................2-51
Table 3-1 Monitoring wells located within the Alapaha River Basin ...................................3-1
Table 3-2 Stage and discharge measurements available for the
Alapaha River and Alapaha Rise .......................................................................3-3
Table 3-3 Available precipitation data in the Alapaha River Basin .....................................3-3
Table 3-4 Population Descriptors for Hydrologic Data from the
Alapaha River at Jennings ...............................................................................3-50
Table 3-5 Population Descriptors for Hydrologic Data from the
Alapaha River at Jennings ...............................................................................3-53
Table 4-1 List of fish species recorded in the Georgia

portion of the Alapaha River. Data obtained from the
Georgia Department of Natural Resources standardized
sunfish sampling. Species listed in alphabetical order by
scientific name. Sampling was conducted in 1998 and 2000 ..........................4-17
Table 5-1 Summary of velocity and depth preferences for taxa chosen
for the Ecological Analysis step of the Ecosystem Function Model..................5-10
Table 5-2 Percentile distributions of the Baseline and proposed
MFL flow duration curves (FDCs) (Figure 5-9) .................................................5-17
Table 6-1 Comparison of Proposed Baseline and MFL FDCs for the
Alapaha River at Jennings .................................................................................6-3
xi
EXECUTIVE SUMMARY
In September 2002, the Governing Board of the Suwannee River Water Management District
(District) initiated the effort to develop MFLs for the Alapaha River.
This technical report presents the data and analyses that provide technical support for the
establishment and adoption of Minimum Flows and Levels (MFLs) for the Alapaha River, a
tributary of the Suwannee River. The goals for these MFLs are:
To implement the intent and policy of the Governing Board of the Suwannee River Water
Management District;
To satisfy the requirement of state water law and policy.
Chapter 373.042, Florida Statutes (F.S.) specifies that:
(1) Within each section or the water management district as a whole, the Department
(Florida Department of Environmental Protection) or the district Governing Board
shall establish the following:
(a) Minimum flow for all surface watercourses in the area. The minimum flow for a
given watercourse shall be the limit at which further withdrawals would be
significantly harmful to the water resources or ecology of the area.
(b) Minimum water level. The minimum water level shall be the level of groundwater
in an aquifer and the level of surface water at which further withdrawals would be
significantly harmful to the water resources of the area.
Subsequent language in the statute (Chapter 373.042(1), F.S.) provides guidance that the
Governing Board shall use the best information available, and that the Board may consider
seasonal variations and the protection of nonconsumptive uses in establishing MFLs.
The Alapaha River is one of three major tributaries of the Suwannee River in Florida. The
Alapaha River is separated from the Suwannee estuary by the Middle and Lower Suwannee
Rivers, for which MFLs are being established.
The Alapaha can be characterized as a southeastern coastal plain, blackwater stream which
originates in the coastal plain of Georgia, west of the Okeefenokee Swamp. The total length of
the river is 130 miles, of which 22.6 miles are located in Florida. The majority of the Alapaha
River Basin, which comprises 1840 square miles, is located in Georgia. The Alapaha River is a
scenic and relatively undeveloped river within Florida. The reach within Florida has several
interesting characteristics that add to its importance. Upstream of State Route (SR) 150, the
river is perennial and incised into a scenic, rock-bound channel. Approximately three miles
downstream from the SR 150 bridge, the river enters a reach characterized by sinkholes that
capture much of the flow during moderate- to low-flow conditions. As a result, the majority of
the river bed in Florida is dry much of the time. Discharge of water captured by the sinkholes is
through two large springs that discharge into the Suwannee River. These springs (Alapaha
Rise and Holton Rise and Creek) support discharge and ecological values in the Suwannee
River.
Three types of analyses were performed to determine which would be the most conservative
protector of the water resource values. An analysis was performed using the wetted perimeter
approach as an estimate of the amount of habitat available to aquatic organisms under different
flow conditions. Fish passage analysis was used to determine the minimum flow necessary to
allow 0.60 feet for fish passage through the most restrictive cross sections of the river. The
xii
Ecological Functions Model (EFM) was utilized to evaluate the minimum flow necessary protect
instream habitat conditions. The conclusions from the three types of analyses are summarized
below:
1. The Ecosystem Functions Model results proved to be the most conservative protector
from significant ecological risk to the target biota, upstream of the capture zone near
the SR 150 bridge. The EFM results suggest a low flow MFL of 115 cfs as measured at
the Jennings USGS gage is protective of habitats preferred by the target biota.
2. A second MFL for mid-level flows is also proposed at 800 cfs. This mid-level MFL
satisfies the requirements for fish passage over several shoals in the lower Alapaha
River and maintains the historic connectivity regime between the Alapaha River and the
Suwannee River.
3. The wetted perimeter analysis results were less critical than the EFM and fish passage
results for the Alapaha River.
Proposed MFL for the Alapaha River at Jennings

In observance of the low flow MFL of 115 cfs, a shift will not be allowed at flows below this level;
thus, the low flow MFL functions as a control point on the MFL-adjusted flow-duration curve.
The establishment of a mid-range flow MFL of 800 cfs thus yields two control points on the flow
duration curve. Conceptually, the establishment of a mid-range flow MFL of 800 cfs for the
Alapaha River should be interpreted as follows: a decrease in the frequency of flows at 800 cfs
of 15% from historically-observed flow frequency is the maximum allowable deviation from
baseline levels.
Additional policy guidance is provided in the State Water Resources Implementation Rule
regarding MFLs (Chapter 62-40.473, Florida Administrative Code [F.A.C.]), indicating that . . .
consideration shall be given to the protection of water resources, natural seasonal fluctuations
in water flows or levels, and environmental values associated with coastal, estuarine, aquatic,
and wetlands ecology. . . . These environmental and water resource values may include:
a) Recreation in and on the water;
b) Fish and wildlife habitats and the passage of fish;
c) Estuarine resources;
d) Transfer of detrital material;
e) Maintenance of freshwater storage and supply;
f) Aesthetic and scenic attributes;
g) Filtration and absorption of nutrients and other pollutants;
h) Sediment loads;
i) Water quality; and
j) Navigation.
It was determined in the evaluation of the best available information that the water resource
value that provided the best opportunity to establish a MFL protective of all the identified
applicable water resource values was fish and wildlife habitats and the passage of fish.
Hence, even though there was not quantitative information available to discretely evaluate all
the applicable water resource values, the MFL recommended for the protection of significant
harm to fish and wildlife habitats and the passage of fish will be protective of the less
conservative water resource values by a qualitative comparison.
xiii
TAB 1
1.0 INTRODUCTION
This technical report (Report) presents the data and analyses that provide technical support for
the establishment and adoption of Minimum Flows and Levels (MFLs) for the Alapaha River.
The goals for these MFLs are:
To satisfy the requirement of state water law and policy.

To implement the intent and policy of the Governing Board of the Suwannee River Water
Management District.
1.1 State of Florida Law Pertaining to the Establishment of MFLS
Chapter 373.042, Florida Statutes (F.S.) specifies that:

(1) Within each section or the water management district as a whole, the Department
(Florida Department of Environmental Protection) or the district Governing Board
shall establish the following:
(a) Minimum flow for all surface watercourses in the area. The minimum flow for a
given watercourse shall be the limit at which further withdrawals would be
significantly harmful to the water resources or ecology of the area.
(b) Minimum water level. The minimum water level shall be the level of groundwater
in an aquifer and the level of surface water at which further withdrawals would
be significantly harmful to the water resources of the area.
Subsequent language in the statute (Chapter 373.042(1), F.S.) provides that the Governing
Board shall use the best information available, and the Board may consider seasonal
variations and the protection of nonconsumptive uses in establishing MFLs.
Additional guidance is provided in the State Water Resources Implementation Rule regarding
MFLs (Chapter 62-40.473, Florida Administrative Code [F.A.C.]), indicating that ...
consideration shall be given to the protection of water resources, natural seasonal fluctuations
in water flows or levels, and environmental values associated with coastal, estuarine, aquatic,
and wetlands ecology .... These environmental and water resource values may include:
a) Recreation in and on the water;

b) Fish and wildlife habitats and the passage of fish;
c) Estuarine resources;
d) Transfer of detrital material;
e) Maintenance of freshwater storage and supply;
f) Aesthetic and scenic attributes;
g) Filtration and absorption of nutrients and other pollutants;
h) Sediment loads;
i) Water quality; and
j) Navigation.
This constitutes the statutory and policy framework for the scope of work to establish MFLs for
the Alapaha River.
1-1
1.2 Project Scope
In October 2004, the Governing Board of the Suwannee River Water Management District
(District) initiated the effort to develop MFLs for the Alapaha River. The study area (Figures 1-
1a and 1-1b) includes those portions of the Alapaha River that are located within Florida.
1.3 Water Body Regulatory Designations
The Alapaha River is a scenic and relatively undeveloped river within Florida. The reach within
Florida has several interesting characteristics that add to its importance. Upstream of State
Route (CR) 150 (Figure 1-1b), the river is perennial and incised into a scenic, rock-bound
channel. Approximately three miles downstream from the CR 150 bridge, the river enters a
reach characterized by sinkholes that capture much of the flow during moderate- to low-flow
conditions. As a result, the majority of the river bed in Florida is dry much of the time. These
unusual flow conditions are of local interest and recreational value.
Discharge of water captured by the sinkholes is through two large springs (Alapaha Rise and
Holton Rise and Creek) into the Suwannee River. The discharge from these resurgences
supports discharge and ecological values in the Suwannee River.
The Suwannee River is widely regarded as a river system with high conservation value. In a
study using data from the National Rivers Inventory (NRI), Benke (1990) identified the
Suwannee as one of 42 large, intact river drainages remaining in the U.S. He defined these
as rivers with more than 124.2 miles (200 km) of length that are unaffected by any major dams,
flow diversions, or navigation projects. These 42 river systems cumulatively represented only
2% of the total length of river reaches in the NRI database. Based largely on Benkes work,
Noss et al. (1995) designated large intact streams and rivers in the U.S. as Endangered
Ecosystems, which they defined as ecosystem types which have experienced an 85-98%
decline in the existence of high-quality, intact examples. In similar fashion, a report on U.S.
river ecosystems by The Nature Conservancy (Master et al., 1998) classified the
Suwannee/Santa Fe drainages as critical watersheds to protect freshwater biodiversity.
Moreover, the federal government has designated portions of the Suwannee River; not the
Alapaha as Critical Habitat for Gulf sturgeon, a federally threatened species. Existing state
designations recognize the Suwannee as a river system of both regional and statewide
importance. The Suwannee is recognized as a system having high conservation and
recreational value, through designations such as Outstanding Florida Water (OFW) and Aquatic
Preserve.
The Suwannee River has been designated an Outstanding Florida Water (Chapter. 62-
302.700[9][i][34], F.A.C.). This designation is conferred to waters of the state with exceptional
recreational or ecological significance (Chapter 62-302.700[3], F.A.C.).
While the Alapaha River has not been designated as a resource of concern, its scenic and
recreational values and importance as a tributary to the Suwannee River warrant MFL
protection. As discussed in subsequent sections, the Alapaha drains underground for
significant portions of the year. As such, protection of water flow and overland discharge during
wet periods is also important.
1-2
.
PULASKI MONTGOMERY
DOOLY
DODGE WHEELER TOOMBS
Cordele
WILCOX
CRISP TELFAIR
JEFF DAVIS
APPLING
BEN HILL
TURNER
IRWIN
COFFEE BACON
WORTH
TIFT
PIERCE
ATKINSON
BERRIEN
BRANTLEY
COLQUITT
COOK
WARE
LANIER
CLINCH CHARLTON
BROOKS LOWNDES
ECHOLS
JEFFERSON
HAMILTON
MADISON
Legend BAKER
SUWANNEE COLUMBIA
Okefenokee Swamp
7.5 3.75 0 7.5
TAYLOR LAFAYETTE Alapaha River Basin
Miles
Figure 1-1a. Total extent of the Alapaha drainage basin.

Note that some of the sub-basins in the Alapaha hydrologic unit are internally drained.
1-3
Jennings
Georgia
Alligator Creek
.
" CR 150 Florida
Dead River
Alapaha River Jasper

SR 6
Legend
Hydrography
Suwannee River Major Roads

Alapaha Rise
0 0.5 1 2
" Sasser Landing
Miles
Figure 1-1b. Extent of the Alapaha River Basin in Hamilton County, Florida.
There are no springs of sufficient magnitude or use on the Alapaha to warrant spring-specific
MFL development. MFLs will be developed for the Alapaha Rise and Holton Creek Rise
resurgences of the Alapaha River as part of MFL development for the upper Suwannee River.
1.4 Relevant Environmental and Water Resource Values
As noted in Section 1.1, Chapter 62-40.473, F.A.C. provides policy guidance regarding
establishment of MFLs. In particular, this section of Floridas Water Policy lists ten specific
environmental and water-resource values that may be considered in setting MFLs. Some are
more relevant to the study area than others.
1.4.1 Method of Identification of Relevant Environmental and Water Resource Values
All ten resource values are initially considered when developing recommended MFLs. Figure 1-
2 illustrates the method used to identify which of the ten values are relevant in terms of MFL
development. The process can be divided into three stages, with the first two taking place
concurrently and throughout the effort to identify the recommended MFLs for the water body.
1-4
DATA EVALUATION PHASE EWRV EVALUATION PHASE
Obtain All Available and Evaluate Each EWRV for

Applicable Data Relevance to MFL Water Body
EWRV
Evaluate Data Relative to YES Relevant to
Applicability to EWRVs MFL Water
Body?
Do Data NO
Reflect a NO
Relationship No Further Action
to Flow or
Stage?
MFL DEVELOPMENT PHASE

YES
Utilize Data to Identify
Conditions for Applicable
EWRVs
Condition and Analyze Data
Identify Limiting EWRV(s) That

Cause Significant Harm
Recommend MFLs to Avoid

Significant Environmental or
Water Resource Harm
EWRV = Environmental or
Water Resource Value
Figure 1-2. Flow chart illustrating the method used to identify the Environmental and Water Resource Values
(EWRV) that are limiting for MFL development on a water body.
1-5
Environmental and Water Resource Value Evaluation Phase As shown in Figure 1-2, the
Environmental and Water Resource Value (EWRV) Evaluation Phase begins with an initial
evaluation of each of the ten values to identify those which are relevant to the water body. Not
all EWRVs are applicable to every water body. For example, protection of estuarine resources
is not necessarily applicable to an inland water body that is either not connected to an estuarine
system or that is distant from a downstream estuary by other water bodies for which MFLs have
been developed to protect the estuarine system. The latter case is appropriate to inland riverine
water bodies within the Suwannee River Basin because the Lower Suwannee River MFL has
been set to protect the Suwannee Estuary. In this phase, each of the ten EWRVs is evaluated
and only those which show no relevancy to the water body are removed from future
consideration. This process only removes EWRVs with obvious lack of relevancy, such as
estuarine resources for upland lakes or streams.
The Data Evaluation Phase is concurrent with EWRV evaluation and involves accessing of all
available and potentially relevant existing data. These data are compared to the relevant
EWRVs and a determination is made as to whether the EWRV data are related to flow or stage
of the MFL water body. If the data are considered invalid or if they do not provide a flow- or
stage-related relationship to a EWRV, they are removed from consideration. If the data are
considered relevant and flow- or stage-related, they are further utilized to refine the MFL.
Finally, the MFL Development Phase brings together all data and data analyses for the purpose
of MFL development. Subsequently, the data and conclusions are again considered in terms of
EWRVs to determine if any appropriate EWRVs were overlooked and determine which EWRVs
limit availability of water and serve as criteria for MFL development.
As part of this process for the Districts MFL-establishment process, environmental and water-
resource values evaluation matrices are prepared to identify potential target values, as defined
by Chapter 62-40.473 F.A.C. (Table 1-1). Developing matrices serves to focus the evaluation,
shape the types of analyses needed to complete the MFL process, and provide a framework for
tracking the MFL development process (Figure 1-2). This ranking process is initiated after
compilation and review of all available data. Each ranking is based upon review of the available
data and the collective experience of the evaluation team in establishing MFLs.
Target values are those that potentially have the highest probability of restricting the amount of
water available for the water body. As an example, if the fish passage criterion is: 1) applicable,
2) has existing or available data, and 3) exhibits a relationship to stage and/or flow then that
value becomes a significant factor for the proposed MFL. This value assessment procedure is
flexible, and new target criteria can emerge during the study of the waterbody.
1-6
1.4.2 Application of the EWRV Review Process
Each of the EWRVs was considered in the development of the MFL. Those that had available
and reliable data and were related to flow were given more detailed consideration. A summary
of the considerations for each EWRV is provided below:
a. Recreation in and on the water. This water-resource value is considered relevant to the
Alapaha River. The upper, perennial reaches of the river are utilized for canoeing and
kayaking. District lands adjacent to the river provide access for hiking and other outdoor
activities. The dry portion of the river has been utilized in the past for off-road vehicular
traffic, although this practice is now forbidden, however there is no available information
on recreational use of the river as it relates to flow.
b. Fish and wildlife habitats and the passage of fish. This water-resource value is
considered relevant for the Alapaha River MFLs. Because of shoals in the perennial
portion of the river and the seasonally dry lower reach of the river, fish passage is of
concern. Major emphases of studies conducted to support the Alapaha River MFLs were
on the significant shoal habitats of the upper Alapaha, opportunities for fish populations to
interact with the Suwannee during periods of high Alapaha River discharge (see Chapter
4 in this report) and how hydrologic conditions structure habitats within the river system.
c. Estuarine resources. This water-resource value is not considered relevant for the
Alapaha River. The Suwannee River estuary is approximately 135 miles downstream
from the mouth of the Alapaha and its rises. Therefore, while discharge from the Alapaha
River contributes to the Suwannee River flow, MFLs set for the Lower Suwannee River
protect the estuary.
d. Transfer of detrital material. It is well established that a principal food base in aquatic and
wetland ecosystems is decaying plant material, collectively termed plant detritus or
simply detritus. Transport of this material from the river floodplain wetlands to the river
channel is an important source of food material for riverine invertebrates. This water-
resource value is relevant to the Alapaha River MFLs, however there is no available
information relating detritus to flow for this system.
e. Maintenance of fresh-water storage and supply. This water-resource value refers to the
long-term maintenance (i.e., sustainability) of water storage and supply capability of the
water body. The result of the protection of this value by MFL establishment is to ensure
that, over time, the ability of the water body to serve as a supply source for existing and
future legal permitted users is preserved without causing significant harm to the water
resource or ecology of the area. This water-resource value is considered relevant to the
Alapaha River MFLs, and it is considered in more detail in Chapter 3. Establishment of an
MFL for a water body implicitly establishes potential water availability.
f. Aesthetic and scenic attributes. This water-resource value is closely linked to (a) above,
pertaining to recreation, in that part of the recreational value of a waterbody is the
aesthetic experience. Aesthetic and scenic attributes are considered relevant to the
establishment of MFLs for the Alapaha River, however there is no available information
on the aesthetic and scenic attributes of the river as they relate to flow.
1-7
g. Filtration and absorption of nutrients and other pollutants. This water-resource value is
considered relevant to the Alapaha River MFL. The role of wetlands in maintenance of
water quality is well-established (Mitsch and Gosselink, 1986). By allowing for settlement
of suspended particulates, uptake of nutrients by plants, and sequestration of some
contaminants in sediments, wetlands help protect water quality. However there is no
available information relating filtration and absorption of nutrients and other pollutants for
the river as it relates to flow.
h. Sediment loads. This water-resource value is considered somewhat relevant to the

Alapaha River MFL. Available evidence (Lawn, 1989) indicates that the lower, ephemeral
reach of the Alapaha carries substantial sediment loads. Most of the rivers sediment load
is carried at higher flows, primarily as a result of periodic flooding of a frequently dry
riverbed. Sediment transport is important in the maintenance of geomorphic features
(bed forms) and their associated ecological communities in the lower river, however there
is no available information relating sediment loads to flow for this system.
i. Water quality. This water-resource value is considered relevant to setting MFLs on the
Alapaha River. Because of the capture of stream flow by the sinkholes south of the CR
150 bridge, groundwater quality is influenced by river water quality (Ceryak, 1977). The
main water-quality considerations were dissolved oxygen, color, and turbidity in relation to
surface-water inflow to the aquifer system. Surface-water quality effects on important
aquatic habitats and fauna were generally considered in Chapter 4.
j. Navigation. This water-resource value was not considered to be relevant to the Alapaha
River MFLs, in that the system is not a waterway that supports commercial shipping or
barge traffic. Passage by recreational vessels, canoes, etc. was considered under the
Recreation in and on the water value, above.
Based on the preliminary screening (Table 1-1), the following resources were investigated to
identify the limiting conditions for MFL development:
Fish and wildlife habitats and the passage of fish,

Maintenance of freshwater storage and supply, and
Water quality.
.
1-8
Table 1-1
MFL DECISION MATRIX: ALAPAHA RIVER
Preliminary
Data Analysis: Potentially
Resource at Resource Related to Significant
Potential Criteria Risk Value Legal Factors Rank Available Data Flow? Criterion?
Notes 1 2 3 4 5 6 7
Recreation in and on the water 1 2 1 4 1 Y N

Fish and wildlife habitats and the
2 2 1 5 2 Y Y
passage of fish
Estuarine resources 1 1 1 3 1 N N
Transfer of detrital material 1 1 1 3 1 Y N

Maintenance of freshwater storage
2 2 1 5 3 Y Y
and supply
Aesthetic and scenic attributes 2 2 1 5 1 Y N
Filtration and adsorption of
1 2 1 4 1 Y N
nutrients and other pollutants
Sediment loads 2 2 1 5 1 Y N
Water quality 2 2 1 5 3 Y Y
Navigation 1 1 1 3 1 N N
Notes:
1. Evaluation of the level to which the resource is at risk. 1 = low risk, 2 = medium risk, 3 = high risk
2. Evaluation of importance of the criterion with respect to resource. 1 = low importance, 2 = medium importance, 3 = highly important
3. Legal constraints on resource, such as endangered species, Outstanding Florida Water, etc. 1 = low, 2 = medium, 3 = high
4. Sum of columns 1, 2, and 3. Indicates overall importance of criterion to MFL development.
5. Evaluation of available data for use in development of MFL based on the criterion. 0 = no data available, 3 = abundant and relevant data
available
6. Evaluation as to whether criterion is related to flow or level in resource. (Yes or No)
7. Evaluation as to whether criterion is potentially significant for MFL development. (Yes or No) To be determined after evaluation of priority
criterion related to flow.
1-9
TAB 2
2.0 INTRODUCTION TO THE SUWANNEE RIVER BASIN AND STUDY AREA
The Alapaha River is one of three major tributaries of the Suwannee River in Florida. As such,
the following discussions begin with an overview of the Suwannee River Basin. The
discussions then focus on that part of the Suwannee Basin relevant to the Alapaha River
minimum flow and level (MFL).
2.1 Suwannee River Basin
2.1.1 Physical Setting of the Suwannee Basin
The Suwannee River Basin encompasses 9,950 mi2 (25,770 km2) in Florida and Georgia
(Figure 2-1; Franklin et al., 1995). The Suwannee is the second largest river system in Florida
by drainage area and mean annual flow (Figure 2-1; Table 2-1). Major tributaries of the
Suwannee River are the Withlacoochee and Alapaha Rivers, which are mostly located in
Georgia, and the Santa Fe River in Florida. In total, approximately 57% of the Suwannee River
basin is in Georgia.
The Suwannee is a low-gradient stream, with an average gradient of 0.4 feet per mile. Table 2-
1 presents general characteristics of this complex river system.
Table 2-1. Descriptive data on the Suwannee River and its major sub-basins (Franklin et al., 1995,
and Berndt et al., 1996).
Basin Area Total Florida Gradient Average
(mi2) Length Length (ft/mile) Flow
(miles) (miles) (ft3/sec)
Suwannee River** 9,950 235 206.7 0.42 10,540**
Withlacoochee River 2,360 120 30.0 2.32 1,714
Alapaha River 1,840 130 22.6 1.80 1,674
Santa Fe River 1,360 79.9 79.9 1.90 1,608
** - includes the contributions of the Withlacoochee, Alapaha and Santa Fe sub-basins
The physiographic setting of the Suwannee River Basin (Allan, 1995; Berndt et al., 1996) acting
in conjunction with regional climatic characteristics controls water chemistry and hydrologic
characteristics of the river system. The river basin lies entirely within the Southeastern Coastal
Plain (Berndt et al., 1996). Major physiographic provinces in Florida include the Northern
Highlands and Gulf Coastal Lowlands physiographic regions (White, 1970; Ceryak et al., 1983;
Figure 2-2).
Characteristics of the Northern Highlands include gently rolling topography, generally from 100-
200 feet above mean sea level (msl). Soils typically range from sand to clayey sand. Clayey
sediments in the subsurface serve as a base for a surficial aquifer and retard infiltration of
rainwater into the underlying Floridan Aquifer System. The result is abundant surfacewater
features (streams, lakes and ponds) throughout the Highlands.
2-1
Figure 2-1. Suwannee River Basin in Florida and Georgia. Basins shown are USGS hydrologic
units (Kenner et al., 1967).
2-2
Figure 2-2. Physiographic regions in the SRWMD and regional hydrography in relation to the
Suwannee River Basin in Florida. Data sources include White (1970); Ceryak et al. (1983); SRWMD
data.
2-3
The Gulf Coastal Lowlands are characterized by elevations from sea level to about 100 feet
above MSL; relatively flat, karstic topography; and shallow, sandy soils with muck in many
wetland areas. Karst landforms are widespread in the lowlands, with abundant features such as
sinkholes, sinking streams and springs, and a high degree of interconnection between
surfacewater and groundwater systems. Carbonate rock (limestone, dolostone) is at or near
land surface throughout the Gulf Coastal Lowlands. Whereas the surfacewater features in the
Northern Highlands reflect the water table of the surficial aquifer, those in the Gulf Coastal
Lowlands represent the water table in the upper Floridan aquifer system.
A significant geologic region separating the two major provinces is the Cody Scarp, or
Escarpment (Figure 2-2; depicted as a line for illustrative purposes) The Cody Scarp is the most
"persistent topographic break in Florida" (Puri and Vernon, 1964). There can be as much as 80
feet of relief along the Scarp. The Cody, a karst escarpment, has been highly modified by
marine shoreline processes. The Scarp region is characterized by active sinkhole formation,
large uvalas, poljes and lakes, springs, sinking streams, and river rises (Ceryak et al., 1983).
During average and lower flows, water in the Santa Fe and Alapaha Rivers is completely
captured by sinkholes as it crosses the Scarp. These rivers re-emerge down-gradient as large
springs known as resurgences or river rises. The Withlacoochee River is partly captured as it
crosses the Scarp near Valdosta, Georgia. Due to its size, the Suwannee is the only stream
that is not significantly captured by a sink feature as it cross the Scarp. Upgradient of the
Scarp, surficial drainage has developed with numerous small creeks branching off the upper
Suwannee and its tributaries (Figure 2-2). Below the Scarp, drainage is predominantly internal
and streams that are tributary to the Suwannee system are rare.
Relict marine terraces are important features of the Suwannee basin in Florida. These terraces
were established by different stands of sea level during the Pleistocene (and possibly Pliocene)
Epoch. The terraces stair-step from the Gulf to the Highlands, and the marine and coastal
processes that created the terraces were responsible for deposition of the surficial sands that
mantle the region (Healy, 1975; Schmidt, 1997). Inland and upward from the coast (Figure 2-3),
these terraces include:
Terrace Approximate Elevation Range

Silver Bluff Terrace 1-10 feet above mean sea level (msl)
Pamlico Terrace 8-25 feet msl
Talbot Terrace 25-42 feet msl
Penholoway Terrace 42-72 feet msl
Wicomico Terrace 70-100 feet msl
Sunderland Terrace 100-170 feet msl
Coharie Terrace 170-215 feet msl
Hazlehurst Terrace 215-320 feet msl
The terraces from Silver Bluff to Wicomico occur primarily in the Gulf Coastal Lowlands
physiographic region, while the Sunderland, Coharie, and Hazlehurst terraces are found in the
Northern Highlands.
2-4
Figure 2-3. Marine terraces in the SRWMD in relation to the Suwannee River Basin. Data sources:
USGS topographic GIS data and Healy, (1975).
2-5
2.1.2 Climate of the Suwannee River Basin
The climate of the Suwannee River basin can be described as a mixture of warm temperate and
subtropical conditions. Mean annual temperature in the Florida portion of the basin is 68.6 F
(NOAA, 2002). The maximum and minimum average monthly temperatures are 81.3 F (in
July) and 54.2 F (January), respectively.
Precipitation and evapotranspiration (ET) are the climatic features most significant to long-term
hydrologic conditions in the Suwannee Basin. Average annual rainfall in the Basin is
approximately 53.4 inches (NOAA, 2002) but varies spatially from 46 inches in the upper basin
to over 60 inches near the Gulf coast (Figure 2-4). This precipitation gradient is largely
controlled by the range in latitude of the basin (equivalent to approximately 200 miles) and the
proximity of the lower third of the basin to the Gulf of Mexico (NOAA, 1972).
Year-to-year rainfall is rarely comparable to the average annual spatial differences. In the area
covered by the NOAA North Florida Climatic Division, annual (calendar year) rainfall has varied
from a low of 35.5 inches (1955) to a high of 77.9 inches (1964). Figure 2-5 shows the long-
term (104 year) rainfall conditions for the north Florida region. The data were smoothed with a
LOESS-type smoothing algorithm as implemented in TableCurve 2D (AISN Software, 2000). As
shown, the smoothed curve suggests that a drier period existed in the first half of the 20th
Century, with wetter conditions subsequently prevailing through the 1990s.
The month-to-month variation in rainfall is as important to understanding the Suwannees

hydrology as annual rainfall. Figure 2-4 shows the typical monthly rainfall pattern at three
locations in the Suwannee River Basin. As with annual rainfall, there is a gradient in seasonal
climatic conditions from the northern to southern regions of the basin. The seasonal pattern is
strongest in the south where a pronounced wet season occurs in the summer months (June
through September). In this area, summer rainfall is associated with localized, convectional
thunderstorms or periodic tropical weather systems (hurricanes, tropical storms). The pattern
weakens in the middle and northern parts of the basin (compare Usher Tower to the Jasper and
Tifton insets, Figure 2-4). More northerly portions of the basin are characterized by lower
average annual rainfall and a weakened seasonal pattern with precipitation that is more evenly
distributed between the warmer and cooler months. Winter rainfall to the north is somewhat
higher than to the south. Winter precipitation events are due to mid-latitude frontal weather
systems with individual rainfall events that are usually more widespread.
Rates of evapotranspiration (ET) in the region have been estimated with a variety of direct
measurements and/or computational methods. The average annual ET pattern shown in Figure
2-6 is estimated from computed reference ET for Gainesville (Jacobs and Dukes, 2004)
multiplied by monthly crop coefficients for pasture (Jacobs and Satti, 2001). Reference ET is
the potential ET from a short, well-watered grass crop. The resulting mean annual ET is 40.8
inches, with the largest mean monthly value of 5.20 inches in June and a minimum of 1.3 inches
in December. The monthly rainfall values in Figure 2-6 are the North Florida Climatic Division
means (NOAA, 2002).
2-6
Figure 2-4. Average annual and monthly rainfall patterns in the Suwannee River Basin (Data:
NOAA, 2002).
2-7
90
Twelve-month total rainfall for the North FL climate division for
12 Month Running Average
the period 1900 through 2003. Rainfall totals are running
averages, and are plotted at the first month of the 12-month Period Average
period. Number of stations varies over the Period of Record. LOWESS Smoothed (50%)
80
Missing Data*
70
Rainfall (Inches)
60
50
40
*Missing data for 1930 was
estimated from long-term
monthly means for use in the
LOWESS smooth
30
1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000
Year
Figure 2-5. Twelve-month total rainfall for the North Florida climate division for the period 1900 to 2003. Rainfall totals are running
averages, and are plotted at the first month of the 12-month period Data: NOAA (2005).
2-8
8
Rainfall
Reference ET
Rainfall Excess
Rainfall Deficit
6
Depth (inches)
0
Jan Feb Mar Apr
Jun Jul May Aug Sep Oct Nov Dec
Month
Figure 2-6. Mean monthly rainfall and reference evapotranspiration in the north Florida region.
Data: NOAA (2002); Jacobs and Dukes (2004); Jacobs and Satti (2001).
Figure 2-6 indicates potential months of net rainfall surplus and/or deficit. During the cooler
winter months, a water surplus can exist that serves to recharge the groundwater system.
During late spring, a rainfall deficit can occur. Utilization of soil moisture (Fernald and Purdum,
1998) and late frontal systems can offset this effect. In the summer, the situation reverses, with
rainfall typically exceeding ET. However, for climate-affected activities, such as agriculture, the
scattered nature of summer convective rainfall events combined with excessive to well-drained
soils often result in site conditions that require supplemental irrigation.
2-9
2.1.3 Geology of the Suwannee River Basin
This section describes the geologic and groundwater systems of the Suwannee River Basin.
Carbonate rock (limestone and/or dolostone) as much as 5,000 in feet thickness exists in the
subsurface of the basin. These strata, which are primarily Tertiary in age, make up the Florida
Platform. The Floridan aquifer system is found within these strata and in similar strata in
Georgia, the Carolinas, and portions of Alabama. The Floridan aquifer portion of this carbonate-
rock platform ranges from about 600 feet to 1,700 feet in thickness (Miller, 1982).
The extent and elevation of the upper surface of the limestone are depicted in Figure 2-7. The
upper surface of the Tertiary limestone ranges from sea level to 90 feet above msl throughout
most of the basin. The limestone begins dipping to the northeast in the northeastern corner of
the District. This dip is about 20 feet per mile, and the top of the limestone reaches a depth of
about 300 feet below sea level in the eastern corner of the District (Figures 2-7 and 2-8). Figure
2-8 illustrates details of the elevation of the top of the Tertiary limestone within the District and
the Suwannee River Basin.
Table 2-2 presents the lithostratigraphic (geologic formation) as well as the hydrostratigraphic
(aquifer system) nomenclature used to characterize the shallow geologic and hydrogeologic
units in the District.
The uppermost geologic unit consists of the Pliocene- and Quaternary-aged

(Pleistocene/Holocene) surficial sand deposits. These deposits are undifferentiated and may
include shell and clay horizons. They were primarily formed by deposition associated with
marine terraces and by erosion and chemical weathering of pre-existing strata.
Table 2-2. Generalized lithostratigraphic column and aquifer systems in the Suwannee River
Basin.
LITHOSTRATIGRAPHIC (ROCK) NOMENCLATURE AQUIFER
SYSTEM SERIES FORMATION SYSTEM
Quaternary Holocene/Pleistocene Undifferentiated Sands Surficial
Tertiary Pliocene Undifferentiated Sands Surficial
Intermediate
Hawthorn Group Aquifer System
Tertiary Miocene
St. Marks Formation and Confining
Beds
Tertiary Oligocene Suwannee Limestone Upper Floridan
Ocala Limestone
Tertiary Eocene Avon Park Limestone Upper Floridan
Oldsmar Limestone
Mid-Floridan
Tertiary Paleocene Cedar Keys Formation
Confining Unit
2-10
Figure 2-7. Extent of the limestone unit bearing the Floridan aquifer system in the southeastern
U.S. Fault line labels indicate: U = Uplift; D = Downlift. Adapted from Miller (1982).
2-11
Figure 2-8. Elevation of the upper surface of the Tertiary limestone strata that constitute the
Floridan aquifer within the District. Adapted from Allison et al. (1995).
2-12
The Miocene Hawthorn Group is present in the northern and northeastern portions of the
District. It consists of interbedded clay, sand, and carbonate strata (Scott, 1988).
While the Miocene and Plio-Pleistocene strata are predominantly composed of siliciclastic
materials (sand, clay, silt) interbedded with carbonate-rich strata, the underlying strata are
predominantly composed of limestone and/or dolostone. These formations include (from top, or
youngest, to bottom, or oldest) the Oligocene Suwannee Limestone, Eocene Ocala, Avon Park,
and Oldsmar formations, and the Paleocene Cedar Keys Formation (Miller, 1997). These strata
comprise the upper Floridan aquifer and, where present, the mid-Floridan confining unit (Table
2-2). The Ocala Limestone, the uppermost section of the Floridan in the majority of the Basin, is
also the source of the majority of groundwater pumpage. The Suwannee Limestone overlies
the Ocala in places, and ranks second in water production District-wide.
Figure 2-9 is a geologic east-west cross section that depicts the relationships of these
formations. The Suwannee Limestone overlies the Ocala Limestone from the Gulf to the
Suwannee River in the west. The Suwannee Limestone is more dolomitic than the Ocala
Limestone within the District. East of the Suwannee River, the Suwannee Limestone is
generally missing. The Hawthorn Group overlies the Ocala and thickens as the Ocala dips to
the east in the eastern two-thirds of the District.
2.1.4 Regional Aquifer Systems
The uppermost aquifer within the District is the surficial aquifer (Table 2-2). The surficial aquifer
occurs within the undifferentiated, Plio-Pleistocene, marine-terrace sands. This aquifer is only
present in the northern and eastern parts of the District where the underlying Hawthorn Group
provides an effective aquitard, which minimizes recharge to the underlying Floridan aquifer.
The surficial aquifer is found locally in the Northern Highlands (Tallahassee Hills west of the
Withlacoochee River) Province, and where water is perched over clays within the San
Pedro/Mallory Swamp complex in Taylor, Lafayette, and Dixie counties. The surficial aquifer is
locally utilized for domestic well water. However, because of dissolved organics, color, odor,
and iron problems, water quality is generally poor and undesirable.
The Hawthorn Group (Table 2-2) includes the Intermediate Aquifer and Confining Beds System.
The strata act primarily as aquitards within the District, but thin layers of gravel, sand, and
carbonate rock form localized aquifers that are capable of producing water to small-yield wells.
The upper Floridan aquifer extends throughout Florida, coastal plain Georgia and portions of the
coastal plain in Alabama, North Carolina and South Carolina (Figure 2-7). The limestone unit
begins along the Fall Line, where Coastal Plain sedimentary rocks lap against the metamorphic
rocks of the Piedmont Province in central Georgia. The upper surface of the limestone dips
easterly and southerly from the Fall Line in central Georgia. The rock surface elevation is about
300 feet above MSL along the Fall Line and dips to elevations lower than 600 feet below MSL in
southeastern Georgia (Miller, 1982). Within the District, the top of the Upper Floridan aquifer
ranges from approximately 100 to +100 feet above MSL (Figure 2-8).
2-13
Figure 2-9. Generalized geologic cross section of the region. Adapted from Ceryak et al. (1983).
2-14
Figure 2-10 depicts the regional potentiometric surface for the upper Floridan aquifer in the
District in May 1976. The contour lines depict the elevation of the water table where the
Floridan is unconfined and correspond to the elevation to which water would rise in wells where
the aquifer is confined. The general direction of flow can be estimated by drawing flow lines that
are perpendicular to the lines of equal potential from high to low potentials. The head pressure
caused by elevation differences in the potentials drives movement of water in the aquifer. The
typical flow rate through the aquifer is estimated to be a few feet per day.
The Floridan aquifer system is primarily composed of limestone and dolostone, and the
movement of water through the aquifer is via both conduit flow (flow through fractures,
caverns, etc.) and diffuse flow (flow through intergranular pore spaces in the rock). As such,
water quality is generally excellent because of extensive dilution, chemical interactions with the
rock matrix, and mechanical filtration.
The salt-water/fresh-water transition zone is the wedge-shaped groundwater zone where fresh
groundwater flows seaward, up and over saline water related to the Gulf of Mexico. The
transition zone is characterized by upward movement and mixing of fresh water with saline
water. The position of the transition has been roughly delineated by sodium and chloride data
along the Gulf of Mexico (Upchurch, 1990), and it has been defined by geophysics within a 20-
kilometer radius around the mouth of the Suwannee River (Countryman and Stewart, 1997).
Shallow aquifer water within about 5 miles of the Gulf coast tends to have relatively higher
concentrations of sodium, chloride and potassium; however, the chloride concentration does not
exceed 25 mg/L, (Copeland, 1987). Well depths in the larger coastal communities range from
85 feet to 170 feet below land surface without a significant increase in sodium, chloride or
sulfate concentrations.
The degree of confinement of the upper Floridan aquifer is a critical factor in aquifer dynamics.
Poorly confined areas tend to be rapidly recharged, while highly confined areas may receive
minimal recharge on an annual basis. The District has compiled a hydrogeologic classification
based on the degree of confinement of the Floridan aquifer system (Figure 2-11) by combining
and evaluating the physiography, geology, and hydrogeology (SRWMD, 1982). The classes of
confinement are as follows.
Class 1 Unconfined. Class I conditions exist where the Floridan is unconfined, is the only
aquifer present, and the carbonate rock is at or near land surface. Where the limestone is not
exposed, the Floridan is usually covered by porous sand. The limestone is porous and
permeable, exhibiting a high degree of secondary porosity that has been enhanced by a
fluctuating water table. Due to the porous nature of the rock and sand, rainwater recharges the
aquifer directly. Recharge rates in this region range from 16 to 31 inches annually (Grubbs,
1998). Surfacewater features usually represent exposures of the water table in the unconfined
Floridan aquifer.
Class II - Semi-confined. Class II conditions exist where the Floridan aquifer is semi-confined
on top by discontinuous, leaky, clay beds. The Class II area in Gilchrist, Alachua and Levy
counties coincides with the Waccasassa Flats and the Class II area in Madison, Taylor, Dixie
and Lafayette counties coincides with the San Pedro Bay/Mallory Swamp region. Because of
reduced recharge, streams drain the Waccasassa Flats and the San Pedro Bay, and there are
lakes on the edges of these features. The Class II
2-15
Figure 2-10. Potentiometric surface of the Floridan aquifer in May 1976. Adapted from Laughlin
(1976); Rosenau and Meadows (1977); Fisk and Rosenau (1977).
2-16
Figure 2-11. Confinement conditions of the Floridan aquifer system in the region. Adapted from
SRWMD (1982).
2-17
area that extends southeast from Suwannee County to Columbia County is the transition zone
that parallels the Cody Scarp. This area is characterized by sinking streams, sinkhole lakes that
periodically drain into the Floridan, and numerous steep-sided sinkholes. Recharge rates to the
Floridan in this region are variable (Grubbs, 1998) and highly localized in location.
Class III Confined. The Class III area is characterized by deeper and confined portions of the
Floridan aquifer. Confinement is a result of at least 80 feet of Hawthorn Group clay overlying
the Floridan. Recharge rates to the Floridan in this region average 12 inches or less annually
(Grubbs, 1998). Confinement creates artesian conditions, and water levels in wells that
penetrate these aquifers usually rise to within 15 feet of land surface.
The surficial aquifer locally overlies the Floridan in the Class II and in most of the Class III
areas, (Figure 2-11). The surficial aquifer consists of unconfined, saturated sand and ranges up
to 55 feet in thickness. The water table is a subdued replica of the topography and is at, or
near, land surface. It coincides with surfacewater levels observed in the swamps, lakes, and
ponds. Streams in these areas drain the surficial aquifer in addition to removing surface runoff.
The surficial aquifer is recharged directly by rainfall and water level fluctuations are directly
related to the amount of rainfall.
As suggested by Figure 2-11, recharge to the Floridan is highly variable. In Class III areas
recharge is limited. The Cody Scarp is an area of generally moderate to high recharge owing to
the presence of sinking streams that flow off the confined, Class III areas (i.e., the Northern
Highlands) of the District and the presence of large sinkholes. A similar pattern exists in the
transition from Class II to Class I regions west of the Suwannee River and in eastern Levy
County (Figure 2-11, Copeland, 2005). Recharge is generally high in the Class I (Coastal
Lowlands, etc.) because of the thin deposits that overlie the limestone of the Floridan and the
presence of many sinkholes.
Areas defined by their high potentiometric surface elevations (Figure 2-10) vary in origin. In
general, they reflect locations within the District where the hydraulic conductivity (permeability)
of the Floridan is relatively low, and groundwater flow is, therefore, slow. The reduction in the
ability to effectively drain water from the aquifer, results in the potentiometric highs in spite of
the low relative recharge. Because of focused recharge on the Cody Scarp and the margins of
other areas where recharge is limited, the margins of the potentiometric highs are supported by
high recharge.
The total fluctuation of the Floridan aquifer potentiometric surface in the basin ranges from zero
to 40 feet in the Alapaha River Basin in the northern part of the Suwannee River Basin (Collins
and Freeman, 1996). There is less than 15 feet of total fluctuation in at least two-thirds of the
District and there is less than 5 feet of total fluctuation along the coast. Average annual
fluctuation is less than 4 feet for approximately two-thirds of the District.
2.1.5 Land and Water Use in the Suwannee River Basin
2.1.5.1 Land Use and Population Characteristics
A summary of land cover/land use conditions (based on 1994 aerial photography) in the Florida
portion of the Suwannee River Basin is shown in Table 2-3. Major human land uses in the
basin in Florida include managed pine forests and agriculture. Available information indicates
that these two uses also dominate land cover in the Georgia portion of the basin (Berndt et al.,
1996). Collectively, residential, commercial and industrial land uses comprise less than 6% of
2-18
the total land use in Florida. The other dominant land cover types in Florida are upland and
wetland forests in a largely natural or relatively less-disturbed condition.
Table 2-3. Land use/land cover conditions in the Florida portion of the Suwannee River basin,
based on 1994 NAPP aerial photography (Source: SRWMD data).
Category Acres %
Residential (all types) 153,324 5.5
Commercial (shopping, office parks, 6,186 0.2
malls, motels, campgrounds, etc.)
Industrial 3,296 0.1
Mining 39,278 1.4
Institutional (prisons, military facilities, 4,031 0.1
schools, churches, hospitals, etc.)
Recreational (golf courses, race tracks, 2,409 0.1
marinas, parks, etc.)
Other developed uses (land being 22,992 0.8
developed, cleared land in urban areas)
Agriculture (pasture and row crops) 584,754 20.9
Agriculture (groves) 4,751 0.2
Agriculture-other (dairy, poultry, hogs, 21,408 0.8
nurseries, aquaculture, etc.)
Non-forested uplands (shrubland, coastal 32,106 1.1
scrub, etc.)
Forested uplands 426,120 15.2
Managed pine forests 1,001,541 35.8
Streams and lakes 33,017 1.2
Artificial water bodies (dug ponds, 5,822 0.2
flooded rock pits, etc.)
Forested wetlands 420,265 15.0
Herbaceous wetlands 16,870 0.6
Disturbed lands 670 <0.1
Infrastructure (airports, power line 21,267 0.8
corridors, sewer and water treatment
facilities, roads)
Population density in the basin averages 29.8 persons per square mile, which is well below the
statewide average of 239 persons per square mile (U.S. Census Bureau, 2002). The two
largest private employment sectors are the forest products industry (pulp manufacturing, lumber
milling, and related silvicultural activities) and phosphate mining and processing. The largest
single source of employment in the region is government, with slightly over half of the total
workforce in the region working for local, state, or federal governments. Major government
employers include local school systems and county governments, the Florida Departments of
Corrections and Transportation, and the federal Veterans Administration.
Most of the point source discharges to the river are located in Georgia. These point-sources are
primarily municipal waste-water discharges. The three major point-source discharges are
phosphate processing facilities, which discharge indirectly via Hunter and Swift Creeks on the
upper Suwannee; a pulp mill located in Clyattville, GA, which discharges via Jumping Gully
Creek to the Withlacoochee River in Florida; and a poultry processing plant, which discharges
directly to the Suwannee River near the Withlacoochee confluence.
2-19
Relative to other areas of Florida, urban non-point sources of water pollution are fairly low
intensity and dispersed. The largest urban area in the drainage basin is Valdosta, GA, which
lies adjacent to the Withlacoochee and Alapaha Rivers. In Florida, relatively urbanized areas
along, or adjacent to, the river or its tributaries include the towns of White Springs, Dowling
Park, Branford, Fanning Springs, Ft. White, and High Springs.
2.1.5.2 Water Use
Estimated water use in the District in 2000 (Table 2-4) was 314 million gallons/day (mgd; WRA,
2005), which equates to about 486 cfs. Water use patterns in the District somewhat mirror land
use. Agricultural irrigation accounts for a large fraction of the existing and projected water use,
although commercial/ industrial is also a large overall use, principally due to phosphate mining
and processing and once-through cooling water for power generation (Marella, 2004; WRA,
2005). By 2020 and 2050, agriculture and industrial water uses are predicted to continue being
the largest uses in the District (WRA, 2005). Total water use in the District is projected to be
approximately 547 mgd in 2020 (which equates to about 846 cfs), and 895 mgd in 2050 (1,385
cfs).
Table 2-4. Summary of current and projected water use in SRWMD (Sources: SRWMD data; WRA
2005).
Water Use Category Existing (2000) Projected (2020) Projected (2050)
Public supply (utilities) 16 mgd 25 mgd 41 mgd
Domestic (self-supplied) 15 25 41
Commercial/Industrial** 190 312 505
Agriculture 91 182 305
Recreation 2 2 4
TOTAL 314 mgd 545 mgd 896 mgd
** - includes commercial, industrial, mining, and power generation
Spatial patterns in existing permitted water use are shown in Figure 2-12. This indicates that a
large proportion of the permitted water use in the District is within the Suwannee basin. Total
water use in 2000 for counties entirely or partly within the Suwannee River Basin in Florida was
approximately 259 mgd, which is 82% of the estimated 314 mgd total District water use.
2-20
Figure 2-12. Map showing permitted water use patterns in the SRWMD. Each symbol represents
the sum of the Average Daily Rate of Withdrawal (ADR) within each 1 mi.2 section.
2-21
2.2 Suwannee River
2.2.1 Surfacewater Hydrology
The hydrology of the Suwannee River Basin is driven by climate, and it is modified by the
topography, physiography, geology, and land cover characteristics of the drainage area. This
section of the report describes rainfall/runoff relationships and spatial and temporal patterns in
river flow. These patterns are the primary driving forces that shape the ecological
characteristics of the river and estuary (Poff et al., 1997).
2.2.1.1 Annual Yield
The annual yield of the Suwannee River is the amount of water discharged to the Gulf of
Mexico. Discharge for the Suwannee is determined by river flow as measured by the U.S.
Geological Survey (USGS) stream gaging program at the most downstream, long-term river
gage (Suwannee River near Wilcox USGS Station Number 02323500). Approximately 97
percent of the basin drainage area is upstream of this gage. Mean daily discharge at Wilcox is
10,166 cfs (Table 2-5), which is equivalent to 14.8 inches of annual runoff from the basin area
(Franklin et al., 1995). Since the average annual rainfall across the basin is 53.35 inches
(Section 2.2), about 28 percent of the mean annual rainfall is discharged as runoff to the Gulf of
Mexico. The remainder of the rainfall, about 39 inches annually, is utilized either as ET or
consumptive use. This estimate corresponds well with the ET estimate of 40.8 inches
presented in Section 2.1.2.
Table 2-5. Discharge Statistics of the Suwannee River at Wilcox (USGS Station Number
02323500), Levy County, Florida.
Cold Season
Annual Warm Season (cfs, November
Metric (cfs) (cfs, May October) April)
Average 10,166 8,993 11,325
Standard Deviation 6,678 4,968 7,858
Maximum 84,700 40,400 84,700
75th Percentile (P75) 12,600 11,300 14,600
Median 8,040 7,620 8,620
25th Percentile (P25) 5,640 5,470 5,920
Minimum 1,070 1,970 1,070
Basin discharge varies over time as shown in Figure 2-13, which shows annual mean flows
superimposed over daily flows at the Wilcox gage. Year-to-year variability in the annual means
is quite evident. During the wettest year on record (1948), discharge was about two to three
times the long-term average. Conversely, the driest recorded year (2002) was about 3 times
less than the long-term average.
The frequency or return period of annual flow (also called the recurrence interval) is also of
interest. The return period is defined as the average number of years between events for
magnitudes equal to or greater than that specified. Figure 2-14 illustrates the flow duration
curve from which exceedance probabilities were defined.
2-22
100000
Discharge (cfs)
10000
Daily
Annual Mean
Mean Annual
1000
1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000
Year
Figure 2-13. Daily and annual discharge (1942-2003) for the Suwannee River near Wilcox
(USGS Station Number 02323500).
100000
Discharge (cfs)
10000
1000
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Exceedance Probability
Figure 2-14. Daily and annual discharge (1942-2003) for the Suwannee River near Wilcox
(USGS Station Number 02323500).
2-23
The annual median discharge (exceedance probability of 50 percent; 2 year return period) is
about 8,040 cfs. The 10 year drought condition (exceedance probability of 90 percent) specified
in Chapter 373.0361(2)(a)(1) as a level-of-certainty planning goal for water supply needs is
4,390 cfs, or about 55 percent of the annual median discharge. Inter-annual variability in
discharge is largely a function of annual rainfall (Figure 2-15). As shown in Figure 2-15, the
best fit of annual relationship of discharge and rainfall is obtained when annualized discharge is
lagged behind rainfall by approximately four months (annual rainfall determined from July
through June and annual discharge from November through October data).
25,000
1948
20,000
Mean Annual Discharge in cfs
(November through October)
15,000
10,000
2
y = 7.6424x - 283.9x + 4352.9
2
R = 0.8398
5,000
-
35 40 45 50 55 60 65 70 75
Total Annual Rainfall in inches
(July through June)
Figure 2-15. Relationship between annual rainfall and discharge for the Suwannee River near
Wilcox (USGS Station Number 02323500).
2.2.1.2 Spatial Flow Patterns
Annual discharge from a basin is related to drainage area (Linsley et al., 1982). The
relationship between drainage basin area and unit discharge assists in understanding spatial
patterns in stream flow. Figure 2-16 shows data from gages on the Suwannee River and
tributaries with 10 or more years of record, and illustrates that long term annual stream flow
throughout the basin varies linearly with drainage area. For main-stem river sites, annual
discharge per unit area (unit discharge) varies from 0.76 to 1.58 cubic feet per second per
square mile (cfsm), with an average of 1.09 cfsm for the entire basin as represented by the
Wilcox gage (Table 2-6).
2-24
100,000
10,000
Mean Annual Streamflow (cfs)
1,000
100
y = 0.9096x
R2 = 0.9817
10
1
1 10 100 1000 10000
Drainage Area (sq. miles)
Figure 2-16. Relationship of drainage area and mean annual discharge for the Suwannee Basin
for gages with 10 or more years of systematic record. Data source: USGS.
Table 2-6. Summary of hydrologic characteristics at flow gaging sites along the Suwannee River
and its major tributaries (from Franklin et al., 1995 and Water Resources Data, GA, 1996). Data are
annual summaries.
Unit
Mean Median Max. Min.
Station Name Discharge
(cfs) (cfs) (cfs) (cfs)
(cfsm)
Suwannee River at Fargo, GA 1,041 450 3,512 60 0.83
Suwannee River at White Springs, FL 1,840 727 6,810 155 0.76
Alapaha River at Statenville, GA 1,082 392 3,280 127 0.77
Withlacoochee River near Pinetta, FL 1,720 620 5,360 236 0.81
Suwannee River at Ellaville, FL 6,530 3,950 19,700 1,300 0.94
Suwannee River at Branford, FL 7,050 5,010 19,300 1,950 0.89
Santa Fe River at Worthington Springs, FL 437 143 1,160 55 0.76
Santa Fe River near Ft. White, FL 1,600 1,330 3,110 724 1.58
Suwannee River near Wilcox, FL 10,540 8,430 24,600 4,290 1.09
2-25
Flow is more variable in the upper portions of the Suwannee and Santa Fe basins (Figure 2-
17A). Flow may vary by 2-3 orders of magnitude in these areas, which are primarily fed by
runoff. Flow is higher but less variable in the lower reaches of these rivers (Figure 2-17B),
varying generally within one order of magnitude. Part of this difference in flow regime is a
function of increasing drainage area contributing to flows at the downstream gage sites. For the
Suwannee system, however, the reduced variability also results from the increased importance
of groundwater inflow from the unconfined Floridan aquifer system adjoining the middle and
lower river reaches.
A. Stream hydrology - Upper Suwannee Drainage (above Cody Escarpment)
100000 100000
Suwannee River at White Springs Santa Fe River near Worthington Springs
Mean Monthly Streamflow (cfs)

10000 10000
1000 1000
100 100
10 10
1 1
1941 1949 1958 1966 1974 1982 1990 1999 1941 1949 1958 1966 1974 1982 1990 1999
Year Year
B. Stream hydrology - Lower Suwannee Drainage (below Cody Escarpment)
100000 100000
10000 10000
1000 1000
100 100
10 10
Suwannee River near Wilcox Santa Fe River near Fort White
1 1
1941 1949 1958 1966 1974 1982 1990 1999 1941 1949 1958 1966 1974 1982 1990 1999
Year Year
Figure 2-17. Mean monthly discharge at four USGS gaging sites on the upper (A) and lower (B)
Suwannee and Santa Fe Rivers, reflecting stream hydrology in the upper and lower portions of
the drainage (after Mattson et al., 1995).
2.2.1.3 Seasonal Flow Patterns
Heath and Conover (1981) recognized the existence of a climatic river basin divide in Florida
that approximates the sub-basin boundaries of the lower Suwannee and Santa Fe Rivers
(Figure 2-18). Streams, north and west of the climatic divide exhibit high flows in the late
winter/early spring, with late spring and fall low flows. Streams south of the climatic divide
exhibit high flows in the late summer/fall, with spring low flows. Streams lying along the climatic
divide tend to exhibit a mixture of both of these patterns (a bimodal pattern of floods in the
spring and fall). More recently, Kelly (2004) reconfirmed these hydrologic patterns in streams in
Florida, which he termed the northern river pattern (spring flooding), the southern river
pattern (fall flooding), and the bimodal pattern (both spring and fall flooding).
2-26
Figure 2-18. Climatic river-basin divide of Heath and Conover (1981). River pattern data from
Kelly (2004). Note that the Alapaha River follows the Northern River Pattern.
2-27
These temporal flow patterns are driven in part by climatic characteristics. The Suwannee
drainage falls in the transitional climatic area between the warm, temperate climate of the
southeastern U.S. and the subtropical climate of the Florida peninsula. Higher, late winter/early
spring rainfall, and lower ET in the northern part of the basin (Section 2.1), drives the spring
flooding, while high summer rainfall in combination with tropical weather events creates the
southern river flooding pattern in peninsular Florida.
Figure 2-19 shows mean monthly discharge for several long-term gages with at least 60 years
of record in the Suwannee Basin. The data are expressed as a proportion of the mean total
annual discharge. The distinct late winter/spring flood is evident, particularly at the sites in the
northern portion of the basin. The two gauging sites in the Santa Fe River drainage basin
(Worthington Springs and Ft. White) exhibit more of the bimodal pattern, as they lie along the
climatic divide discussed above.
Temporal patterns in discharge are also affected by geologic characteristics. Downgradient of

the Cody Escarpment (Figure 2-2), the Suwannee and its tributaries receive increasing amounts
of groundwater discharge from the Floridan aquifer. This groundwater inflow results in
substantially higher base flow, which proportionally dampens the more pronounced spring
flood peak seen in the upper basin. This dampening affect results in a more uniform
hydrograph downstream (Figure 2-19; cf. the Santa Fe River near Ft. White and Suwannee
River near Wilcox gage data).
2.2.1.4 Tidal River and Estuary
The Alapaha River is separated from the Suwannee estuary by the Middle and Lower
Suwannee Rivers, for which MFLs are being established. Therefore, estuarine resources are
not pertinent to establishment of the Alapaha River MFL. This brief discussion is included to
provide a context for understanding the Suwannee System.
The Suwannee estuary consists of the lower reach of the river, two major branches (East and
West Passes), Suwannee Sound, and the adjacent coastal waters stretching from Horseshoe
Beach to the Cedar Keys (Figure 2-20). The approximate upstream boundary of the estuary
extends about 10 miles upstream from the river mouth. Moreover, the tidally-influenced reach
of the river (the tidal river) extends further upstream. During 2002 when record low discharges
occurred in the lower river, daily stage at the Suwannee River near Bell (USGS Station Number
02323000) at River Mile 55 varied by as much one foot, depending on tidal phase and wind.
More typically, the tidal range at Bell is 0.25 to 0.5 feet. McPherson and Hammett (1991)
indicated that the normal tidal reach of the Suwannee extended upstream 26.7 miles (43 km)
from the river mouth, or about 12% of the total length of the river.
Mean tidal range in the estuary is about 3.4 feet (McNulty et al., 1972; Tiner, 1993). Tides are
mixed semi-diurnal, typically with two unequal high and two unequal low tides occurring each
day, separated in time by approximately 6.2 hours (Leadon, 1985). Low tide in the estuary
occurs first near Cedar Key with the result that typical Suwannee fresh-water plumes flow
southward along the coast (Leadon, 1985).
Depths in the Suwannee Sound average 6.6 feet, with depths to about 20 feet in the river
channels of East and West passes (Figure 2-20).
2-28
Figure 2-19. Gage locations and mean monthly discharge patterns at selected long term
surfacewater gages in the Suwannee River Basin. Discharge expressed as a proportion of mean
annual discharge at each gage. Data source: USGS flow data.
2-29
Figure 2-20. Major features of the Suwannee estuary. Data sources: USGS aerial imagery and
SRWMD map data.
2-30
East and West passes divide the flow from the Basin with about 64 percent discharging through
West Pass and 36 percent through East Pass. In fact, flow in the passes is dominated by tidal
effects, superimposed on net fresh-water discharge.
2.2.1.5 Chemical Characteristics
Physiographic characteristics exert a strong influence on river hydrology and water chemistry in
Florida. Because of the geologic and physiographic changes the Suwannee experiences in its
course through north central Florida, the river exhibits important longitudinal changes in water
chemistry (Ceryak et al., 1983; FDER, 1985). The changes in these characteristics may best be
described by recognizing five regions or ecological reaches of the Suwannee River in Florida
(Figure 2-21):
Reach 1. Upper River Blackwater Reach 4. Lower River Calcareous

Reach 2. Cody Scarp Transitional Reach 5. Tidal Riverine
Reach 3. Middle River Calcareous
Water chemistry in the Suwannee changes in a unique way from upstream to downstream
(Bass and Cox, 1985). The upper river (Reaches 1 and 2) is an acidic, blackwater stream, with
waters of low mineral content (low hardness) and high color (Figures 2-22 and 2-23). As the
river progresses downstream (Reaches 3, 4, and 5), it receives increasing amounts of water
from the Floridan aquifer, which changes river water quality to a clear, slightly colored, alkaline
stream (Figures 2-22 and 2-23).
These natural chemical gradients influence the ecology of the river in many ways. In terms of
overall biological production, the upper river tends to be more oligotrophic, while the lower river
is more productive.
Total organic carbon concentrations are higher in the upper reaches of the river (Hornsby et al.,
2000), largely due to the dissolved and total organic carbon associated with the high water
color. Nutrient concentrations (dissolved nitrogen and phosphorus) are low, generally near
detection limits (Hornsby et al., 2000 and SRWMD data); in the uppermost reach (Reach 1).
The low levels of nutrients in the upper reach contribute to its low biological productivity.
Dissolved nitrogen and phosphorus levels generally increase going downstream. Peak
phosphorus levels are seen in Reach 2, partly as a result of the river crossing the phosphatic
Hawthorn Group exposures and partly due to wastewater discharges from phosphate mining
and processing.
Highest nitrogen levels are seen in the middle and lower reaches (Reaches 3, 4, and 5). A
historical trend of increasing nitrogen has been identified in the middle and lower Suwannee and
lower Santa Fe Rivers (Ham and Hatzell, 1996; SRWMD data). Much of this increase comes
from groundwater discharging via springs along the river corridor (Pittman et al., 1997; Katz et
al., 1999). Areas of elevated nitrate nitrogen have been identified in the upper Floridan aquifer
in these regions (Hornsby and Ceryak, 2004). Sources of this nitrogen are diverse and include
agricultural operations, wastewater sprayfields, areas with dense concentrations of septic tanks,
and storm-water runoff to sinkholes.
The 2004 Florida Water Quality Assessment 305(b) Report (FDEP, 2004) revealed generally
good water quality in the Suwannee River Basin. Portions of the lower river and most of the
estuary were designated as impaired for which they are candidates for total maximum daily
2-31
load (TMDL) establishment. Portions of the upper Suwannee and Santa Fe sub-basins were
indicated to be potentially impaired. These assessments appear to have been based on low
dissolved oxygen (which is partly natural due to groundwater discharge), nutrients (discussed
above), or elevated fecal coliform levels.
Figure 2-21. Map showing the ecological reaches of the Suwannee River in Florida. Source:
SRWMD data and Hornsby et al. (2000).
2-32
Reach 1 Reach 2 Reach 3 Reach 4 Reach 5
120.00
100.00
mg/L as CaCO3
80.00
60.00
40.00
20.00
0.00
0
0
01
04
07
08
10
12
13
14
15
16
24
W
W
SU
SU
SU
SU
SU
SU
SU
SU
SU
SU
SU
Figure 2-22. Plot of mean alkalinity (mg/L as CaCO3) in the five reaches of the Suwannee River in
Florida.
Reach 1 Reach 2 Reach 3 Reach 4 Reach 5

450
400
350
300
250
PCU
200
150
100
50
0
0
0
01
04
07
08
10
12
13
14
15
16
24
W
W
SU
SU
SU
SU
SU
SU
SU
SU
SU
SU
SU
Figure 2-23. Plot of mean color (platinum cobalt units; PCU) in the five reaches of the Suwannee
River in Florida.
2-33
2.2.2 Ecology
2.2.2.1 Aquatic and Wetland Communities
The physical setting described in the previous section is the framework that structures the
ecological communities of the river ecosystem, including those communities in the river channel
and on the adjacent floodplain. On a landscape scale, this linkage is recognized by delineating
stream ecoregions (Griffith et al., 1994), which are regions within which lotic ecosystems
exhibit generally similar morphology, hydrology, and water chemistry and thus support similar
biological communities. The Suwannee River Basin in Florida lies within the following Florida
ecoregions (Griffith et al., 1994):
Southeastern Plains Ecoregion

Tifton Upland/Tallahassee Hills subregion
Southern Coastal Plain Ecoregion

Okeefenokee Swamps and Plains subregion
Central Florida Ridges and Uplands subregion
Gulf Coast Flatwoods subregion
Eastern Florida Flatwoods subregion
Sea Island Flatwoods subregion
These ecoregions and subregions influence, and are influenced by, the hydrology, water
chemistry, and biota of the major ecological reaches of the Suwannee and its tributaries (as
shown in Fig. 2-21). An overview of each of these follows.
2.2.2.2 River Reach Ecology
2.2.2.2.1 Suwannee River Mainstem
Reach 1. Upper River Blackwater Reach. This reach lies within the Okeefenokee Swamps and
Plains sub-region. The river channel in this reach (Figure 2-24) is more deeply incised into the
landscape, as compared to downstream reaches, and varies from 100-160 ft. in width. At base
flows, depths in the channel are mostly < 3 ft. Shoals of exposed clay and shallow sandy runs
are a prominent habitat feature in the river channel along this reach, and the river channel
bottom is generally course sand or exposed clay. Because surficial drainage is better
developed in this part of the Basin, numerous small tributary creeks branch off the river channel.
The river floodplain is inundated only by larger floods (i.e., floods with 5-10 year recurrence
intervals), and flooding duration is often less than 30 continuous days. Plant communities in the
floodplain are mostly upland forests, dominated by natural or planted pine, oaks, magnolia and
hickory. Wetlands in the floodplain are mainly associated with the tributary creeks branching off
the main channel, and consist of cypress and deciduous hardwoods (swamp tupelo, river birch,
ogeeche tupelo, and others). The Suwannee in this reach is a classic, southeastern
blackwater stream (see prior section). Benthic invertebrate communities are dominated by
caddisflies and chironomids. Highest invertebrate densities are found in the shoal habitats
(Bass and Cox, 1985).
Reach 2. Cody Scarp Transitional Reach. In this reach, the river is mostly within the Tifton
Uplands/Tallahassee Hills subregion. The river channel is still incised into the landscape, and
varies from 130-260 ft. in width (Figure 2-24). The channel bottom is still dominated by shallow
2-34
Figure 2-24. Basic geomorphology of the river channel and floodplain and typical plant
communities in each of the five ecological reaches (Figure 2-20) of the Suwannee River.
Adapted from Lynch, 1984.
2-35
Figure 2-24. Continued.
water habitat, with depths 3-6 ft. or less and numerous areas of sandy or rocky shoals. Channel
bottom substrates include medium to coarse sand, exposed clay, and rock (limestone, chert,
dolostone). Some of these shoal areas in the region of the Alapaha Rise and confluence are
critical spawning habitat for the Gulf sturgeon (Sulak et al., 2001). In this region, the river
crosses the Cody Scarp (Ceryak et al., 1983). This is a region, with numerous sinkholes. Karst
features are evident in the river floodplain, which produces high plant diversity due to the
topographic variation. This reach includes the confluences of the Alapaha and Withlacoochee
rivers with the Suwannee River main-stem. Limestone outcrops are prominent along the river
channel throughout this reach, and springs discharge groundwater to the river. Major springs
include White Springs, Suwannee Springs, Holton Spring, Alapaha Rise, Ellaville Spring, and
Lime Spring. Benthic invertebrate communities are dominated by caddisflies, chironomids, and
mayflies. The Alapaha River in Florida is largely in a Reach 2-type environment.
Reach 3. Middle River Calcareous Reach. The third reach of the river exhibits a number of
changes reflecting greater flows and a larger drainage area. This reach crosses the Central
2-36
Florida Ridges and Uplands subregion and the Gulf Coast Flatwoods subregion. The river
channel is wider (260-330 ft. or more), with alternating deeper pool areas interspersed with
rocky shoals. Some limestone crops out along the river channel. The floodplain is inundated
more frequently, and in some areas alluvial features indicating this can be seen (e.g., berm and
swale topography; Figure 2-24). Floodplain plant communities are largely high terrace
bottomland hardwood communities, with live oak, laurel oak, blue beech, American elm, swamp
chestnut oak, and bald cypress. Benthic invertebrate communities are dominated by
chironomids, mayflies, caddisflies and snails. Major springs include Troy Spring, Charles
Spring, Telford Spring, Peacock Springs, Lafayette Blue Spring, Royal Spring, and Little River
Spring.
Reach 4. Lower River Calcareous Reach. Reach 4 of the Suwannee begins at the Santa Fe
River confluence and lies entirely within the Gulf Coast Flatwoods subregion. In this reach, the
river channel is wide (400-500 ft.) with a deep-water channel. No shoals occur in this reach.
The river channel substratum includes coarse sand and exposed limestone. The floodplain has
numerous topographic features caused by fluvial action, including relict levees, oxbow lakes,
and high and low terraces (Figure 2-24). Floodplain plant communities include a diversity of
types, ranging from swamps to bottomland hardwoods. Swamps are dominated by bald
cypress, water tupelo, planer elm, swamp privet, and pop ash. Bottomland hardwood forests
include some of the above, plus live oak, laurel oak, American elm, water hickory, overcup oak,
blue beech, and other broadleaf deciduous hardwoods. Major springs include Rock Bluff
Spring, Hart Spring, Guaranto Spring, and Otter Spring. Benthic invertebrate communities are
similar to those in Reach 3.
Reach 5. Tidal River Reach. This reach, begins at the U.S. 19 bridge at the town of Fanning
Springs. As indicated in the section on hydrology, tidal variation in river stage is evident here at
low flows. This reach also lies entirely within the Gulf Coast Flatwoods subregion. The river
channel approaches 800-1000 ft. in width. River channel substrata include exposed limestone,
medium and coarse sand, and sandy mud in areas of reduced current velocity. The channel is
fringed by tidal, freshwater marsh, which becomes more evident downstream. These marshes
are dominated by wild rice, bulrushes, cattail, pickerelweed, spatterdock, and water hemlock.
Along the outer edge of these marshes, where water depth and sediment conditions permit,
beds of submerged vegetation dominated by eelgrass and spring tape may grow. The
floodplain in the upper portions of this reach includes forest types similar to those seen in Reach
4. As the river nears the Gulf, tidal freshwater swamps (Wharton et al., 1982) and hydric
hammock (Vince et al., 1989) become the dominant forest types. The tidal swamps are
dominated by bald cypress, pumpkin ash, swamp and sweet bay, cabbage palm, red maple,
and swamp tupelo. Hydric hammocks are a wetland forest type unique to Florida, with the
greatest extent occurring in this region of the Florida coast (Vince et al., 1989). These forests
are characterized by a diverse tree canopy. Characteristic species include cabbage palm, laurel
and live oak, sweetgum, sweet bay, swamp bay, southern red cedar, red maple and blue beech.
Two major springs, Fanning Springs and Manatee Springs, occur on this reach. Benthic
invertebrate communities are similar to those in Reaches 3 and 4, although as the river nears
the Gulf, estuarine species begin to appear (i.e., olive nerite snail, red-joint fiddler crab, wharf
crab).
2.2.2.2.2 Santa Fe River
The Santa Fe River drainage encompasses more sub-ecoregions (6) than any other river basin
in Florida. The river drainage lies within portions of the Tifton Uplands/Tallahassee Hills,
Central Florida Ridges and Uplands, Okeefenokee Swamps and Plains, Sea Islands Flatwoods,
2-37
Eastern Florida Flatwoods, and Gulf Coast Flatwoods subecoregions. This landscape diversity
accounts for the high overall biological diversity exhibited in this river system. The upper portion
of the river includes numerous shallow runs, with a sand-bottomed channel, which may become
braided and diffuse in some reaches. Flow in the upper Santa Fe is dominated by surfacewater
runoff. The river is captured by a sink at OLeno State Park, and the river re-emerges about 3
miles downgradient as the Santa Fe Rise. The lower Santa Fe River is heavily influenced by
spring inflow, and is typically clear and alkaline. The upper portions of this lower reach are
mostly shallow and include numerous shoal areas of exposed limestone and beds of
submerged aquatic vegetation (SAV). The lower portion is wider and deeper, with SAV beds
confined to the channel margins. In terms of channel morphology, the lower Santa Fe
somewhat resembles Reach 3 of the Suwannee, although with a narrower river channel. The
channel bottom substrata are mostly coarse sand and exposed limestone. Major springs include
the Ichetucknee Springs group, the Ginnie Springs group, Hornsby Spring, Gilchrist Blue Spring
group, Poe Spring, and Rum Island Spring. Benthic invertebrate communities are characterized
by mayflies, caddisflies, chironomids, amphipods and snails.
2.2.2.2.3 Withlacoochee River
The Withlacoochee River drainage lies mostly within Georgia, in the Southeastern Plains
Ecoregion. The rivers general morphology is that of a low gradient, eastern, coastal plain
stream with a sand-bed channel (Brussock et al., 1985). Using Becks (1965) classification, the
Withlacoochee is a sand-bottom stream. In Florida, the river channel is incised in the
underlying Suwannee and Ocala limestones, and numerous limestone shoals are found in the
channel. Other channel bottom substrata are medium and coarse sand. Water chemistry in the
river is moderately to highly colored, somewhat alkaline, and highly turbid on occasion.
Because of the somewhat higher relief and clay soils found primarily in the Georgia portion of
the watershed, the Withlacoochee carries a higher sediment load than other streams in the
Suwannee drainage (USDA, 1977). Consequently, the river is more of a muddy river than the
Suwannee during higher flows. This sediment load is obvious when viewing the confluence of
the Withlacoochee and Suwannee at higher flows (generally average flow and greater). At
baseflow, the river water is substantially less turbid and more reflective of a southeastern
coastal plain, blackwater stream. The inflow of hard, carbonate-rich groundwater from the
Floridan aquifer at baseflow (via springs and diffuse inflow) contributes to the higher pH and
alkalinity of the water in Florida. Major springs include Blue, Pot, and Suwannacoochee.
Benthic invertebrate communities are dominated by chironomids. Other dominants in the
benthic community include crustaceans (the amphipod Hyalella and grass shrimp,
Palaemonetes paludosus), blackflies (Simulium spp.), aquatic beetles (Coleoptera), caddisflies
(Trichoptera) and mayflies (Ephemeroptera).
2.2.2.2.4 Alapaha River
The third major tributary of the Suwannee is the Alapaha River, the study area for this MFL
document. Its drainage, like the Withlacoochee, lies mostly within Georgia. The physiography
and soils of the drainage are more like those of the upper Suwannee, and it lies almost entirely
within the Southern Coastal Plain Ecoregion. Consequently, the river may be characterized as
a southeastern coastal plain, blackwater stream. When river flows are below average, much of
the river flow is captured by sinkholes about 4 miles south of the Florida-Georgia state line and
the remainder of the river channel in Florida is dry for a substantial portion of a typical year
(Ceryak, 1977). The river re-emerges at the Alapaha Rise (Ceryak, 1977), and possibly at
Holton Spring, both are characterized as blackwater springs. Benthic invertebrate communities
2-38
in the upper, perennial reach of the river in Florida (above the sinks) are dominated by
chironomids, mayflies, stoneflies, and caddisflies.
2.2.2.2.5 Suwannee Estuary
The estuary of the Suwannee River is deltaic (Day et al., 1989), with extensive intertidal areas
ranging from tidal fresh water to polyhaline portions of the estuary. About 6 miles before it
reaches the gulf, the Suwannee branches into West Pass and East Pass (Figure 2-20). These
distributaries flow through a broad delta area that includes Hog Island, Bradford Island, Little
Bradford Island, and the area around Dan May Creek at the mouth of East Pass. The river
empties into a shallow embayment called Suwannee Sound, which is partially enclosed by
Suwannee Reef; a complex of oyster reefs and sand bars extending from north of Wadley Pass
south to near Cedar Key.
The Suwannee River accounts for 60% of the total fresh-water inflow into the Big Bend region of
the Florida coast (Montague and Odum, 1997), which makes it the largest estuary in the Big
Bend. The intertidal wetlands and submerged habitats found throughout this area provide
primary production and habitat for a great many animal species with ecological and economic
value (i.e., those caught commercially or for sport). Spatial and temporal variation in salinity
due to river flow variation is a major environmental influence that structures the plant and animal
community composition of the wetlands on the river delta and the submerged habitats in the
estuary.
2.2.2.2.6 Species and Habitats of Interest
Because the Suwannee Basin coincides, in part, with a climatic transition zone, it is a significant
biogeographic transition zone in Florida. Many species of flora and fauna reach their
southernmost limits of distribution in the U.S. in the Suwannee region. Over half the native
fresh-water fishes found in Florida river systems occur only in, or west of, the Suwannee (Bass
and Cox, 1985; Bass, 1991). A number of plant species reach the southern limits of their
distribution in the southeastern U.S. in the Suwannee region (Clewell, 1985).
Key species of interest (e.g., listed taxa, rare or endemic species) dependant upon aquatic and
wetland habitats in the lower Suwannee are shown in Table 2-7. These are listed as either (1)
endangered or threatened by the U.S. Fish and Wildlife Service (USFWS), (2) endangered,
threatened, or a species of special concern by the Florida Fish and Wildlife Conservation
Commission (FWCC), or (3) Rare and Endangered Biota of Florida published by the Florida
Committee on Rare and Endangered Plants and Animals (FCREPA), or (4) as S1, S2, or S3 by
the Florida Natural Areas Inventory (FNAI).
Additional species of interest, which occur in the Suwannee estuary, are shown in Table 2-8.
These are listed by the National Oceanic and Atmospheric Administration as important
Estuarine Living Marine Resources (ELMR), chosen based on four criteria (Nelson, 1992): 1 -
commercial value (harvested commercially), 2 - recreational value (sportfish), 3 - indicator of
environmental stress, and 4 - ecological value (important forage or food base organisms). Many
are also listed by the Florida Fish and Wildlife Research Institute (FWRI) as Selected Taxa
because of their commercial, recreational or ecological value.
2-39
Table 2-7. Aquatic and wetland-dependent species of interest in the lower Suwannee River study area.
Scientific Name Common Name Federal State FCREPA FNAI TNC
Plants
Lobelia cardinalis Cardinal flower T
Matelea gonocarpa Angle pod T
Peltandra sagittifolia Spoonflower R
Ulmus crassifolia Cedar elm R S1
Zephyranthes atamasco** Zephyr lily
Invertebrates
Caecidotea hobbsi Florida cave isopod S2
Chimarra florida Florida finger-net caddisfly S1
Cincinnatia mica Ichetucknee silt snail SSC S1
Crangonyx hobbsi Hobb's cave amphipod SSC S2-S3
Dolania americana Sand-burrowing mayfly T S1-S2
Medionidus walkeri Suwannee moccasinshell T S?
Poanes viator zizaniae Rice skipper R
Polygonia comma (skipper) R
Pleurobema reclusum Florida pigtoe T
Procambarus erythrops Red-eye cave crayfish SSC R S1
Procambarus lucifugus alachua Alachua light-fleeing cave crayfish R S2-S3
Procambarus pallidus Pallid cave crayfish R S2-S3
Satyrodes appalachia appalachia (butterfly) R
Troglocambarus maclanei MacLane's cave crayfish R S2
Fishes
Acipenser oxyrhynchus desotoi Gulf sturgeon T SSC T S2 Im
Agonostomus monticola Mountain mullet R S3
Ameiurus serracanthus Spotted bullhead S3
2-40
Ameiurus serracanthus Spotted bullhead S3
Cyprinella leedsi Bannerfin shiner S3
Micropterus notius Suwannee bass SSC S2-S3
Notropis harperi** Redeye chub
Reptiles
Alligator mississippiensis American alligator T SSC S4
Caretta caretta Loggerhead sea turtle T T T S3
Chelonia mydas Green sea turtle E E E S2
Lepidochelys kempi Kemp's Ridley sea turtle E E E S1 Im
Macroclemys temmincki Alligator snapping turtle SSC SSC S3
Malaclemys terrapin Diamondback terrapin Im
Clemmys guttata Spotted turtle R
Pseudemys concinna suwanniensis Suwannee cooter SSC SSC S3
Drymarchon corais couperi Eastern indigo snake T T SSC
Nerodia clarkii clarkii Gulf salt marsh snake R S3?
Eumeces egregius insularis Cedar Key mole skink R
Birds
Ajaia ajaja Roseate spoonbill SSC R S2-S3
Aramus guarauna Limpkin SSC SSC S3
Casmerodius albus Great egret SSC S4
Egretta caerulea Little blue heron SSC SSC S4
Egretta rufescens Reddish egret SSC R S2
Egretta thula Snowy egret SSC SSC S4
Egretta tricolor Tricolor heron SSC SSC S4
Nycticorax nycticorax Black-crowned night heron SSC S3?
Nycticorax violacea Yellow-crowned night heron SSC S3?
2-41
Ixobrychus exilis Least bittern SSC S4
Eudocimus albus White ibis SSC SSC S4
Mycteria americana Wood stork E E E S2
Grus canadensis pratensis Florida sandhill crane T T S2-S3
Haliaeetus leucocephalus American bald eagle T T T S3
Elanoides forficatus Swallow-tailed kite T S2-S3
Pandion haliaetus Osprey SSC S3-S4
Pelecanus occidentalis Eastern brown pelican SSC T S3
Haematopus palliatus American oystercatcher SSC T S3
Recurvirostrata americana American avocet SSC S1-S2
Rynchops niger Black skimmer SSC SSC S3
Sterna antillarum Least tern T T S3
Sterna caspia Caspian tern SSC S2?
Sterna maxima Royal tern SSC S3
Mammals
Trichechus manatus latirostris Florida manatee E E E S2 Im
Ursus americanus floridanus Florida black bear T T S2
Microtus pennsylvanicus Florida saltmarsh vole E E E S1
dukecampbelli
Federal and State are species officially listed by the U.S. or State of Florida (respectively); FCREPA=species listed by the
Florida Committee on Rare and Endangered Plants and Animals; FNA I=species listed by the Florida Natural Areas Inventory;
TNC=species listed in Beck et al. (2000). E=endangered; T=threatened; SSC=species of special concern; R=rare; S1=critically
Imperiled in Florida because of extreme rarity; S2=imperiled in Florida because of rarity; S3=rare, restricted, or otherwise
vulnerable to extinction in Florida; S4=apparently secure in Florida; S?=status unknown; Im=imperiled. ** - included due to
restricted distribution in north central Florida or narrow habitat requirements.
2-42
Table 2-8. FWRI "Selected Taxa" and NOAA "Estuarine Living Marine Resources" (ELMR) taxa
found in the Suwannee estuary.
FWRI taxa ELMR taxa
American oyster XX
Common Rangia XX
Bay squid XX
Penaid shrimp (Farfantepenaeus spp.) XX XX
Grass shrimp XX
Blue crab XX XX
Stone crabs (Menippe spp.) XX XX
Bull shark XX
Tarpon XX XX
Ladyfish XX
Alabama shad XX
Gulf menhaden XX
Gizzard shad XX
Bay anchovy XX
Hardhead catfish XX
Sheepshead minnow XX
Gulf killifish XX
Silversides XX
Bluefish XX XX
Crevalle jack XX
Grey snapper XX XX
Red snapper XX XX
Red grouper XX
Gag XX
Sheepshead XX XX
Pinfish XX
Silver perch XX
Sand seatrout XX XX
Spotted seatrout XX XX
Spot XX XX
Atlantic croaker XX
Black drum XX XX
Red drum XX XX
Mullets (Mugil spp.) XX XX
Code goby XX
Pompano XX
Spanish mackerel XX XX
King mackerel XX
Cobia XX
Gulf flounder XX XX
Southern flounder XX
Whiting/kingfish (Menticirrhus spp.) XX
2-43
Communities or habitats of conservation interest in the Suwannee basin are listed in Table 2-9.
These are listed as endangered or threatened by Noss et al. (1995), as imperiled or rare by the
Florida Natural Areas Inventory (FNAI and FDNR, 1990), as a Primary Habitat Target for the
northern Gulf of Mexico by Beck et al. (2000), or as Essential Fish Habitat by the National
Marine Fisheries Service (NMFS, 1999).
Table 2-9. Aquatic and wetland habitats of conservation interest in the lower Suwannee study
area.
USGS FNAI TNC NMFS
Large, intact river systems E
Spring-run stream* S2
Aquatic cave S2
Intact floodplain wetlands* T S3-S4
Tidal freshwater swamp* S3 PT
Tidal freshwater SAV beds* PT efh
Seagrass beds S2 PT efh
Tidal marshes* S4 PT efh
Oyster reefs & bars* S3 PT efh
USGS=ecosystems listed in Noss et al. (1995); FNAI=Florida Natural Areas Inventory listed habitats; TNC=habitats listed in Beck et al. (2000);
NMFS=National Marine Fisheries Service designated Essential Fish Habitat (efh). E= endangered; T=threatened; S2=imperiled in Florida because of
rarity; S3=rare or uncommon in Florida; S4=apparently secure in Florida; PT=listed as Primary Habitat Target for biodiversity conservation; *=target
habitat identified for development of MFL in this report.
2-44
2.3 Alapaha River Drainage Basin and Related Springs
2.3.1 Introduction
As noted in Section 1, the Alapaha River Basin is an important recreational and ecologic
resource. The effects of both the river and its resurgences (springs that discharge significant
amounts of water derived from the capture of Alapaha River flow) on the Suwannee River are
important to the natural and scenic beauty of the area.
Figure 2-25. Rock-bound channel at shoals Figure 2-26. - Rock shoals approximately
area north of the CR 150 Bridge (Figure 1-1b) 1 mile upstream of the CR 150 bridge over
Note the emergent sand bar at left center of the Alapaha River. (Bridge is located at
image. Sasser Landing, near Jennings, Florida
Figure 1-1b.)
The Alapaha River Basin in Florida (Conover and Leach, 1975) encompasses roughly 100
square miles of central Hamilton County (Figures 1-1a and b). This area represents less than
10 percent of the Alapaha drainage basin, which covers approximately 1,700 square miles and
extends northward nearly 100 miles into southern Georgia. That portion of the Alapaha River
Basin within Florida contains approximately 15 sub-basins (Foose, 1981); some of which are
internally drained and do not contribute direct runoff to the Alapaha River.
Figure 2-27. View of the Alapaha River Figure 2-28. Sinkhole in the bed of the
looking north (upstream from the CR 150 Alapaha River near the mouth of the Dead
bridge at Sasser Landing Figure 1-1b). River blind valley. Geologists are
River is at low flood stage. standing at the opening of the sinkhole.
2-45
The Alapaha River begins in southern Georgia near the town of Cordele (Figure 1-1a). From its
headwaters, the river flows southeast through agricultural lands of the Southeastern Plains of
Georgia before turning southward across the Okefenokee Plains (Griffith et al., 2001; Georgia
Department of Natural Resources, 2002). As the Alapaha flows southward, the river flows
through forested areas and wetlands that skirt
the western boundary of the Okefenokee
Swamp (Figure 1-1a). The Alapaha River enters
Florida near the town of Jennings (Figures 1-1b).
North of County Road (CR) 150, the river is
incised into a rock-bound channel (Figure 2-25)
with rock shoals (Figure 2-26) and a narrow
floodplain. The shoals outcrops are primarily
composed of dolostone and sedimentary opal of
the Miocene Hawthorn Group (McFadden,
1982).
Down stream from the shoals, the floodplain

broadens (Figure 2-27) for a short distance. It
then enters a region where swallets (sinkholes
that capture river water and transfer it to the
underlying aquifer) begin to capture a significant
amount of surface flow to the underlying Floridan
aquifer. The development of swallets results
from the thinning of the Hawthorn Group semi-
confining beds by erosion as the river flows
south (Ceryak, 1977). Upchurch (2007)
presents a brief discussion of the Cody Scarp Figure 2-29. View into the sinkhole shown
and how sinking streams and resurgences, such in Figure 2-28. The exposed rock consists
as the Alapaha River swallet-resurgence of limestone and dolostone of the
Statenville Formation (Miocene Hawthorn
system, function.
Group).
Figure 2-30. Dead River during a drought. Figure 2-31. Dead River sink. Note the
In karst terminology, this is known as a rock exposed around the sinkhole and the
blind valley, a valley that transports water drift wood transported to the sink from
to a sinkhole, into which the stream the Alapaha River during higher flow
disappears. conditions.
2-46
Figure 2-32. View looking downstream in Figure 2-33. View of the dry Alapaha
the dry Alapaha River bed at the mouth of River bed downstream of the SR 6 Bridge
the Dead River blind valley. (Figure 1-1b) and within the reach of the
river where sinkholes capture discharge.
During low to moderate flows in the river, surface discharge diminishes until it is entirely
captured by sinkholes and swallets (Figures 2-28 and 29) in the bed of the river southeast of
Jennings (south of the CR 150 bridge).
A major swallet system is associated with a blind valley known as Dead River. Blind valleys
are karst features characterized by flow of surfacewater that is diverted from the mainstem of a
river into a stream channel that terminates in a sinkhole, through which surfacewater recharges
the underlying, carbonate aquifer. Figures 2-30 and 231 depict Dead River and its swallet,
respectively.
Overland flow in the Alapaha River reaches the Suwannee River only during high flows and
Figure 2-34. - Mouth of the Alapaha River Figure 2-35. The Alapaha Rise on the
as seen from the Suwannee at moderate north bank of the Suwannee River. This
low flow. Note the sandy bed incised in normally brown-water spring discharges
limestone bedrock. part of the water recharged to the Floridan
aquifer at the sinkholes upstream on the
Alapaha (Figs. 2-28 through 2-31).
2-47
floods. Much of the time, the lower river is dry owing to the capture of discharge from the upper
river at the sinkholes about 3 river miles south of the CR 150 bridge (Figure 1-1b).
When the lower Alapaha River is dry, large, sandy bed forms are exposed (Figure 2-32 and 2
33). Lawn (1989) showed that these sand bars are mobile during episodes of flooding, and a
small delta of sand extends from the mouth of
the river into the Suwannee River (Figure 2-34).
The river water that enters the aquifer at Dead

River and the swallets in the river bed, discharges
to the Suwannee River through two resurgences
(Ceryak, 1977). These resurgences are the
Alapaha Rise (Figure 2-35), which drains directly
to the Suwannee River and Holton Creek Rise
(Figure 2-36), which drains to the river through
Holton Creek. The locations of these resurgences
are depicted in Figure 1-1b.
The water that drains into the underlying upper Figure 2-36. Holton Spring and the head
of Holton Creek. Holton Spring
Floridan aquifer can be identified within the
discharges water recharged to the
aquifer because of color, odor, and iron content. Floridan aquifer at the Alapaha River
Ceryak (1977) showed that this water spreads sinkholes during high stream flow
over an area of about 50 square miles in the conditions. At low flow, discharge is
aquifer. limited and constitutes Floridan aquifer
water. As such, this resurgence serves
The influence of karst and sinkhole drainage on as an escape route for water that is
the flow in the Alapaha River has important unable to discharge at the Alapaha Rise.
implications for water quality and quantity in the
Florida portion of the Alapaha River Basin. Determination of availability of water as well as
MFLs are challenges given that the lower reaches of the Alapaha River are dry for much of a
typical year, when a significant amount of flow is captured and channeled into the subsurface.
The Alapaha River groundwater basin is characterized by flow toward the river (Figure 2-10)
from the east and west. In Florida, the basin is separated from the Suwannee River Basin on
the east and the Withlacoochee River Basin on the west (Figure 2-37).
2.3.2 Population and Water Use
2.3.2.1 Population Distribution
The Alapaha River Basin is not heavily populated in southern Georgia. According to the 2000
census, approximately 43,724 residents lived in Valdosta, Georgia, the largest center of
population in the watershed (U.S. Census Bureau, 2002). The remaining area is rural and
consists largely of agricultural and undeveloped land. Population statistics indicate that, since
1960, the population in the region has increased approximately 57 percent from approximately
135,000 to 212,000 in 2000 (U.S. Census Bureau, 2002). Even with this growth, however, the
Alapaha River Basin in Georgia retains a decidedly rural character, with a population density of
approximately 64 persons per square mile.
Like southern Georgia, the Alapaha River Basin in north Florida is largely rural. According to
the 2000 census, approximately 1,800 residents lived in Jasper, the largest center of population
2-48
Georgia
Alapahoochee River
50
Florida
Alligator Creek
60
Little Alapaha River
Dead River
50
Withlacoochee River
Alapaha River
HAMILTON
40
!
40
!
! !
!
Alapaha Rise
Approximate boundary
! Un-named springs
of Alapaha
MADISON ground-water basin
! Holton Creek Rise
!! ! !
! ! !! !
Suwannee River ! !!
! ! !!! ! !
! !!
!
! !
!
!
!! !
! !
! !
! Legend !
SUWANNEE ! Spring
! Stream
! Potentiometric contour
(feet above sea leve)
0 0.5 1 2
Lake
Alapaha basin
70
Miles
Figure 2-37. Potentiometric surface of the Floridan aquifer and approximate location of the Alapaha ground-water basin in the vicinity of
the Alapaha River in Florida. Data modified from SRWMD (1995)
2-49
in the Florida portion of the watershed, and approximately 800 residents lived in Jennings (U.S.
Census Bureau, 2002). The remaining area consists of agricultural and undeveloped land.
Population statistics indicate that, since 1960, the population of Hamilton County has increased
42 percent from approximately 7,705 to 10,930 (U.S. Census Bureau, 2002).
2.3.2.2 Land Use
Land use in the Alapaha River Basin was identified using the 1996 USGS Arcview land-use
coverage (Florida Geographic Data Library, 2004, SRWMD) (Figure 2-38). Pine plantations,
upland forests, improved pasture, and row crops cover much of the watershed. Cypress,
wetlands, and swampy areas also cover the upper portions of the watershed to the north of
Jasper. Residential land uses are scattered throughout the watershed and consist mainly of
low-density single-family units and mobile home ranchettes.
Alapahoochee River Georgia
Florida
Jennings Alligator Creek
Dead River
Alapaha River
Jasper
Legend
Stream Watershed boundary
Urban - commercial & Wetland areas

residential
Low density & mobile Upland forests
Alapaha Rise home ranchettes
Row crops Improved pasture
Un-named springs
0 0.5 1 2
Holton Creek Rise Woodland pasture Cypress
Suwannee River !! ! !
Miles
Figure 2-38. Major land uses in the Alapaha River Basin of Florida. Data from the District.
2-50
2.3.2.3 Water Use
According to estimates by Marella (1999), groundwater was withdrawn from the Floridan aquifer
in Hamilton County at the rate of approximately 46.2 million gallons per day (mgd) in 1995.
Agricultural withdrawals, rural self-supplied, and public water-supply systems accounted for
approximately 10.4 percent (4.8 mgd), 1.8 percent (0.8 mgd) and 1.9 percent (0.9 mgd),
respectively, of the total withdrawals in the County (Marella, 1999). Cumulatively, these
withdrawals accounted for only 14 percent of the water use in the County in 1995. The
remainder of water withdrawn from the upper Floridan aquifer system (39.6 mgd) was used for
industrial purposes, namely mining.
As shown by Table 2-10, the largest water user in 2000 in Hamilton County, which includes the
Alapaha River Basin in Florida as well as portions of the Suwannee and Withlacoochee basins,
was in the commercial, industrial, mining, and power sector. Of these, Hamilton Countys
phosphate mines, which are largely within the Suwannee River Basin as opposed to the
Alapaha, constitute the largest user. The total water use is projected to grow by as much as
125 percent by the year 2050 (Table 2-10; Water Resources Associates, Inc., 2004). Most of
this growth is projected to be in the commercial, industrial, mining, and power sector, but a 120
percent growth in domestic self-supply of water and 100 percent growth in public supply are
also projected.
Table 2-10. Estimated Historic and Projected Water Use (mgd) in Hamilton County, Florida
2000 2010 2025 2050
Agriculture 6 8 12 17
Commercial,
Industrial, Mining, 34 42 53 73
Power
Domestic Self
1 1 1 1
Supply
Public Supply 2 1 2 2
Recreation 0 0 0 0
Total Projected
42 52 68 93
Use
Source: Water Resource Associates, Inc., 2004
2.3.3 Topography, Physiography, and Drainage
The topography of the Alapaha River Basin varies considerably. Land-surface elevations range
from less than 50 feet above MSL (mean sea level) near the confluence with the Suwannee
River to elevations in excess of 150 feet above MSL in upland areas along the Florida-Georgia
state line (Figure 2-39). In the immediate vicinity of the Alapaha River, however, elevations are
generally less than 100 feet above MSL. As a result, the river has a low gradient along much of
its course through Hamilton County.
2-51
Georgia
.
Alligator Creek
Florida
Dead River
Alapaha River
Legend
Hydrography
Topographic Contours
50 ft Contour
Suwannee River Alapaha Rise 100 ft Contour
2 1 0 2
150 ft Contour
Miles
Figure 2-39. Topography of the Alapaha River Basin.
2-52
Two major physiographic provinces, the Northern Highlands and Gulf Coast Lowlands (White,
1970), lie within the Alapaha River Basin (Figure 2-40). The Northern Highlands is an upland
area (typically greater than 75 feet above MSL) capped by relatively impermeable, clay-rich
sediments, which results in local surfacewater runoff. The abundance of sinkholes and closed
depressions (Figure 2-41) along the southern margin of the Northern Highlands (i.e., the Cody
Scarp (Puri and Vernon, 1964)) has created a landscape that favors large internally drained
basins, which greatly increase the relative amount of recharge to the upper Floridan aquifer
system. The internally drained basins that lie along the western side of the Alapaha River
watershed, therefore, contribute very little, if any, surfacewater runoff to the Alapaha River.
The Gulf Coast Lowlands lies adjacent to the Northern Highlands and is an area of subdued
topography, underlain by a thin veneer of sandy cover over karstic limestone of the upper
Floridan Aquifer System. The Gulf Coast Lowlands (typically between 25 and 75 feet above
MSL) is a mature karst plain characterized by low recharge and localized areas of discharge,
such as at springs and along the channels of large streams. Recharge is limited because of
high water-table conditions and locally upward groundwater gradients. Sinkholes in the Coastal
Lowlands are typically small in area (Figure 2-41), but they are numerous (Upchurch, 2002).
2-53
Alapahoochee River Georgia
Alligator Creek Florida
Dead River
Northern Highlands &

Cody Scarp
Alapaha River
Gulf Coast
Lowlands Legend
! Spring
Alapaha Rise
Stream
Un-named springs
Sub-basin
0 0.5 1 2
Holton Creek Rise boundaries
!! ! !
Miles
Suwannee River Lake
Figure 2-40. Physiographic regions in the Alapaha River Basin of Florida.
2-54
Georgia
.
Alligator Creek
Florida
Dead River
Alapaha River
Legend
Suwannee River Alapaha Rise Hydrography
2 1 0 2
Closed Depressions
Miles
Figure 2-41. Closed depressions (sinkholes and other karst features) in the Alapaha River Basin in Florida (study area).
2-55
2.3.4 Geology and Hydrology
2.3.4.1 Local Stratigraphy and Geomorphology
Figure 2-40 depicts the physiographic provinces within the Florida portion of the Alapaha River
Basin. The Northern Highlands constitute most of the drainage basin with the transition to the
Gulf Coastal Lowlands (the Cody Scarp) lying in the southern quarter of the basin. Geological
conditions at the transition from the Northern Highlands to the Coastal Lowlands are the primary
reason that the river loses to the groundwater system. Figure 2-42 is a geologic map showing
the stratigraphic units at or near land surface in the Alapaha River watershed.
Throughout the basin, the uppermost stratigraphic unit consists of undifferentiated marine
terrace sand. This sand forms a thin veneer in most areas, but scattered dune and beach ridge
deposits are present within the Alapaha River Basin. The sand derived from erosion of the
marine terrace deposits, especially in cut banks along the river, makes up the sandy bed load of
the river. The marine terrace deposits also constitute the host materials for the surficial aquifer
system in the Northern Highlands.
The uppermost named strata in the Northern Highlands constitute the Miocene Hawthorn Group
(Table 2-2). The Hawthorn Group consists of interbedded phosphatic sand, clay, and dolostone
deposits (Scott and others, 2001). Due to its clayey composition, the relative vertical
permeability of the Hawthorn Group is generally low, so the Hawthorn tends to form an
intermediate confining unit above the upper Floridan aquifer and below the surficial aquifer
system.
The lower portions of the Hawthorn Group (the Miocene Statenville Formation) contain
widespread layers of limestone and dolostone. A sandy limestone that crops out near Dead
River has been mapped as the Miocene St. Marks Formation (Ceryak, 1977), as well. This
carbonate stratum is the first significant carbonate unit encountered by the river as it undergoes
headward erosion. The karst system that captures the river has developed within this unit.
Thick sequences of limestone, including the Statenville and St. Marks formations and older
strata (Table 2-2), are exposed at or very near (i.e., within 10-20 feet) the land surface in many
parts of the watershed, especially in the Gulf Coast Lowlands and along the course of the
Alapaha downstream from Dead River. The uppermost pre-Miocene limestone units in the
study area include the Suwannee and Ocala Limestones of Oligocene and Eocene age,
respectively. Below the Ocala Limestone is the Eocene Avon Park Formation (Table 2-2).
The major carbonate unit in the study area is the Oligocene Suwannee Limestone, which lies
near land surface throughout much of the region and crops out in the river downstream from CR
150 (Figure 2-42). Based on well cuttings, Crane (1986) described the Suwannee Limestone in
the study area as consisting of several lithologies of marine origin: a dark yellowish-brown,
moderately to well-indurated, sucrosic dolomite; a white-to-pale orange, poorly to moderately
indurated, fossiliferous calcilutite; a yellow-gray, moderately to well-indurated, fossiliferous
calcilutite; and a white, moderately to well-indurated, highly porous, and fossiliferous
calcarenite. The upper surface of the Suwannee Limestone is marked by karst features and in
some areas, has been eroded and is no longer present in the subsurface (Crane, 1986).
2-56
Alapahoochee River
Georgia
Alligator Creek Florida
Ths Little Alapaha River
Dead River
Alapaha River
Ts
Qu
Qu
Legend
Qu - undifferentiated
Quaternary deposits
Alapaha Rise
Ths - Hawthorn Group
Un-named springs
Statenville Formation
0 0.5 1 2
Holton Creek Rise
Suwannee River !! ! ! Ts - Suwannee Limestone
Miles
Figure 2-42. Geologic map of the Alapaha River Basin.
2-57
The Eocene Ocala Limestone lies below the Suwannee Limestone, where present. Based on
well cuttings, Crane (1986) described the Ocala Limestone in the study area as consisting of
several lithologies of marine origin. The deepest of these lithologies is a medium to well-
indurated calcarenite composed almost entirely of Miliolid foraminifera. Above this unit lies a
medium to well-indurated calcarenite composed of the foraminifera Operculinoides sp. and
Miliolids. Capping these two lower lithologies is a unit that is described as a poorly to
moderately indurated calcarenite composed of the foraminifera Lepidocyclina sp. Much like the
underlying Avon Park Formation, the upper surface of the Ocala Limestone is highly variable
and karstic (Crane, 1986).
The Eocene Avon Park Formation is the oldest rock unit that crops out in Florida. In the study
area, the Avon Park Formation consists of moderate to well-indurated, sugary dolostone, and
moderately to well-indurated calcilutite, calcarenite and calcirudite. Thin seams of peat are
often associated with the more dolomitized sections of the Avon Park Formation. In deeper,
more calcitic sections of the Avon Park, Miliolids and foraminifers, especially Dictyoconus
americanus, are often present (Crane, 1986). Gypsum is also present in small amounts in the
Avon Park Formation, though it typically occurs several hundred feet below msl in the study
area (Crane, 1986).
The Suwannee Limestone, Ocala Limestone, and the Avon Park Formation comprise the
Floridan aquifer in the Alapaha Basin. The Floridan aquifer is the primary source of water within
the Florida portion of the Alapaha basin. The Alapaha River discharges into the Floridan in the
vicinity of the sinkhole system south of CR 150.
2.3.4.2 Surfacewater Hydrology
Surfacewater features are not abundant in the Florida portion of the Alapaha River Basin owing
to karst activity within the Cody Scarp. In the upper reaches of the basin, surfacewater features
are closely associated with runoff from the Okefenokee Plains (Griffith and others, 2001) in
southern Georgia. The abundance of streams and wetlands in the basin near the Florida-
Georgia border reflects the low permeability of the Hawthorn Group in the Highlands and
Okefenokee Plains of Georgia, high water table, and tendency for surficial aquifer groundwater
to discharge to the surface.
The low surface gradient of the landscape causes much of the surfacewater in the region to
pond on the surface, resulting in sluggish flow in the surfacewater systems. However, as flow
moves southward, towards the Cody Scarp, more and more flow is captured in basins with
sinkhole drainage. In these basins, the surfacewater flows into sinkholes before it reaches the
Alapaha River. Surface flow in the Alapaha River is also captured and funneled into the
subsurface by sinkholes along the bed of the River southeast of Jennings in an area where the
Statenville Formation and Suwannee Limestone lie at or near the land surface (Figure 2-42).
2.3.4.3 Karst and Groundwater Hydrology
Karst - The lower Alapaha River Basin (Cody Scarp and Gulf Coastal Lowlands) is an area of
intensive karst development, characterized by numerous sinkholes, lack of surface drainage,
and undulating topography (Figures 2-39 and 2-41). In karst areas, dissolution has created
enlarged cavities along fractures in the limestone, which eventually collapse or reach the
surface and form sinkholes. Sinkholes capture surfacewater runoff and funnel it underground,
which promotes further dissolution of limestone. This dissolution leads to progressive
2-58
integration of voids beneath the surface over time and allows increasingly larger amounts of
water to be transported through the groundwater system.
Groundwater may flow rapidly through conduits and passages with the limestone or slowly
through minute pore spaces within the rock matrix. Dye-trace studies in Columbia County show
that groundwater near Ichetucknee Springs may travel approximately one mile per day in active
conduits in the Floridan aquifer (Karst Environmental Services, 1997). Similar velocities were
recorded near Sulphur Springs in Hillsborough County (Stewart and Mills, 1984). Studies such
as these clearly indicate show that groundwater has the potential to flow rapidly and traverse
great distances in a short amount of time in karst environments near major springs. Because
the flow in these karst conduits is rapid and direct, dispersion, dilution, and retardation of
contaminants is likely to be minimal and the springs are vulnerable to contamination.
The Alapaha Rise shows rapid responses to recharge and potential for contamination. The
calculated lag time between a recharge event in the river near Dead River and the Alapaha Rise
varies from about 2 to 21 days depending on discharge of the Jennings gage (see Section
3.3.3.1). The lag reflects a period of time sufficient for water to enter storage in the aquifer and
migrate to the resurgences (Alapaha and Holton Rises). Ceryak (1977) showed that river water
invaded a very large area of the aquifer (about 50 square miles), so it is apparent that flow to
the resurgences is not entirely by a single conduit system. The dispersion of colored, river
water in the aquifer is evidence that the conduit system is complex and has a strong lateral as
well as longitudinal flow as it works its way to the resurgences.
Recharge - Recharge to the Floridan aquifer is directly related to the confinement of the aquifer
system. The highest recharge rates occur where the Floridan is unconfined or poorly confined
as in those areas where the aquifer is at or near land surface. Recharge may also be high in
areas where the confining layers are breached by karst features, such as sinkholes in the Cody
Scarp (Figure 2-41) and the sinkholes within the Alapaha River near Dead River.
Other factors affecting recharge rates include the development of surfacewater drainage,
variations in water-level gradients between surfacewater, the surficial aquifer and the Floridan
aquifer, and aquifer permeability. Low recharge rates occur where confining materials overlying
the aquifer retard downward vertical movement of water, or where an upward gradient exists
between the Floridan and surficial aquifers. Figure 2-43 shows the estimated recharge potential
of the Floridan aquifer in the Alapaha Basin (SRWMD, 2001).
Potentiometric Surface - Potentiometric surfaces of the Floridan aquifer in the Alapaha Basin
are shown in Figures 2-10 and 2-37.
Some distinctive features are visible on the potentiometric surface maps. Most importantly, the
spacing between the isopotential lines suggests the development of permeability within the
Floridan aquifer. Note in Figure 2-10 that the isopotential lines are relatively close together
north of the study area, and that they are more widely spaced up gradient (north) and down
gradient (south) of the location where the isopleths are close together near the state line. The
widely spaced isopotential lines north of the state line reflect a well-confined aquifer with low
hydraulic gradients. Work in the Lake City and Live Oak areas (Lawrence and Upchurch, 1976,
1982; Upchurch, 2002) suggests that permeability in the Floridan aquifer is not well developed
under the Northern Highlands and that groundwater flow is impeded because of low hydraulic
conductivities, which results in a low groundwater gradient.
2-59
Georgia
.
Alligator Creek
Florida
Dead River
Alapaha River
Legend
Hydrography
Discharge
High Recharge
Suwannee River Alapaha Rise Moderate Recharge
2 1 0 2
Low Recharge
Miles
Figure 2-43. Recharge potential in the Alapaha River Basin.

2-60
Near the Cody Scarp (just north of the state line on Figure 2-10), the isopotential lines indicate
that the gradient is steeper and that groundwater flow is more dynamic. This is the transition
from lower permeability under the Northern Highlands to higher permeabilities under the Cody
Scarp (Upchurch, 2007) and the Gulf Coastal Lowlands. This is also the area where karst
begins to interact with the river system and recharge is greatly increased.
The widely spaced isolines south of the Scarp, near the mouth of the Alapaha, indicate well-
developed karst with high hydraulic conductivity in the Floridan aquifer (Lawrence and
Upchurch, 1976, 1982; Upchurch, 2002).
Given this potentiometric surface, it is apparent that groundwater flow in the Alapaha River
Basin generally flows toward the river from the east and west (Figure 2-10). The introduction of
surfacewater south of CR 150 reduces the hydraulic gradient and enlarges the groundwater
basin down gradient from the river sinks. Ceryak (1977) showed that recharge events from the
river to the Floridan aquifer temporarily reverse the gradient. Discharge from the resurgences
governs the ultimate gradient during recharge events.
2-61
TAB 3
3.0 HYDROLOGIC ANALYSES
3.1 Overview
The United States Geological Survey (USGS) has collected continuous stage and stream-flow
data at locations on the Alapaha River since as early as 1932. The USGS and District have
funded the network cooperatively since 1975. The period of record for each of these sites
varies by starting date and collection frequency, and some sites have been discontinued and
then re-established at a later date.
This section presents a summary and analysis of the hydrologic data that is available for
determining minimum flows and levels (MFLs) for the Alapaha River in Florida.
3.2 Data Availability
Unless otherwise noted, the District provided all data for this analysis. The data set includes
groundwater levels and use, stream gage data for the Alapaha River and the Alapaha Rise, flow
measurement data for Holton Rise and Creek, and precipitation data.
3.2.1 Groundwater Data
3.2.1.1 Groundwater Levels
The complete record for all monitored wells was provided for Hamilton County. Data exists for
10 wells located within the Alapaha River study area (Figure 3-1). Table 3-1 contains
information on water-level data available for these wells, including the date first and last
measured, the frequency measured, total number of measurements, and minimum and
maximum groundwater levels within each well. Appendix A contains graphs of the complete
data set for each of the wells in the study area.
Of these 10 wells, only two have been monitored on a daily basis for some period, and there are
data gaps in many of these data sets (Table 3-1). The remaining wells have been monitored on
a monthly, quarterly, or yearly basis. Some wells have significant gaps within their monitoring
records.
Table 3-1. Monitoring wells located within the Alapaha River Basin.
Number
of Min Max
First Last Frequency Measur (ft (ft
Well Site ID Aquifer Measured Measured Measured ements msl) msl)
1 +011202001 Floridan 11/01/1976 05/31/2002 Quarterly* 28 29.67 58.69
2 +011216001 Floridan 06/28/1983 05/03/1984 Quarterly 4 33.75 55.05
3 +011222001 Floridan 02/22/2001 02/26/2004 Yearly 4 27.68 38.40
4 +011226001 Floridan 07/26/2001 02/26/2004 Yearly 4 24.24 34.48
5 +021202001 Floridan 01/24/1961 05/13/1996 Monthly* 245 34.91 70.85
6 +021211001 Floridan 07/26/1977 09/20/2004 Daily* 5957 34.88 69.91
7 +021227001 Floridan 06/28/1983 05/03/1984 Quarterly 4 29.99 54.70
8 +021323001 Floridan 11/01/1976 05/10/1990 Quarterly* 23 31.43 62.08
9 +021332004 Floridan 06/12/1989 09/20/2004 Monthly 192 32.40 73.52
10 +021432001 Floridan 11/01/1976 09/22/2004 Daily 8252 33.75 67.74
* There are large gaps in data collection in these data
3-1
.
Georgia
5
Alligator Creek
6
Florida
Dead River
8
7
9 10
1
Alapaha River
2
3
Legend
Monitoring Wells
Suwannee River 4
Alapaha River Basin
2.5 1.25 0 2.5
Hydrography
Miles
Figure 3-1. Location of monitoring wells in the Alapaha River Basin of Florida.
3-2
3.2.1.2 Groundwater Quality
Some of the wells listed in Table 3-1 that are currently being monitored for water levels are also
sampled for geochemical indicators as part of the Districts Water Assessment Regional
Network (WARN). These data are utilized, where appropriate, for source-water identification,
and they are considered with respect to MFL development.
3.2.2 Surfacewater Data

Stage and/or discharge data were utilized from four gages in the Alapaha River Basin (Table 3-
2; Figure 3-2). Table 3-2 contains the time ranges of data collection, the number of direct stage
and discharge measurements, and the number of daily measurements of stage and discharge
for each station. The data are presented graphically in Appendix B.
The most complete and extensive data set is from the Alapaha River near Statenville, GA gage,
provided by the Georgia USGS. The data set for the Alapaha River near Jennings spans
roughly 25 years, though one large gap (~10 years) and numerous smaller gaps exist. The
gage on the Alapaha River near Jasper has never been continuously monitored. Limited
discharge data for the Alapaha Rise are also available.
3.2.3 Precipitation Data

Precipitation data exist for several stations in the vicinity of the Alapaha River Basin. The first
and last date measured, along with the largest rainfall total for a single month at that gage, are
presented in Table 3-3 and locations of the gages are shown in Figure 3-3. The data are
presented graphically in Appendix C. Daily precipitation data was obtained from the National
Oceanic and Atmospheric Administration (NOAA) for the gage at Jasper, located just outside
the Alapaha River Basin. Monthly precipitation data are also available for one site (the Alapaha
Tower; Figure 3-3) within the basin.
Table 3-2. Stage and discharge measurements available for the Alapaha River and Alapaha Rise.
# of # of Daily Values
Stream Gauging Station Available Measurements
USGS Ref. SRWMD Site Period of Stag Discharge Stage Discharge
# ID Description Record e
Alapaha River at 12/10/1931-
02317500 +050010103 728 747 2,727* 26,228
Statenville, GA 02/01/2005
Alapaha River near 02/09/1976-
02317620 +021201001 293 91 5,214 5,540
Jennings 04/14/2004
Alapaha River near 04/06/1948-
02317630 +021332001 151 82 ------- -------
Jasper 08/18/2001
Alapaha Rise near 04/02/1976-
02315648 +011235002 ------- 79 ------- -------
Fort Union 11/20/2003
* Digital data not available prior to 10/01/1997
Table 3-3. Available precipitation data in the Alapaha River Basin.

Station Type First Measured Last Measured Maximum Event (Date)
Alapaha Tower (46) Monthly January 1976 May 2004 16.76 in (July 1991)
Alapaha Tower (246) Data not available
Jasper (NOAA) Daily October 1, 1952 February 25, 2005 10.2 in (April 1, 1962)
3-3
.
" 02317500
(Statenville)
Georgia
02317620 Alligator Creek

(Jennings)
"
Florida
Dead River
02317630
(Jasper) "
Alapaha River
Legend
02315648 " Stream Gages
Suwannee River
(Fort Union) Alapaha River Basin
2.5 1.25 0 2.5
"
Hydrography
Miles
Figure 3-2. Locations of stream gages in the Alapaha River Basin.
3-4
.
Georgia
Alligator Creek
Florida
Dead River
46
246 # NOAA
#
Alapaha River
Legend
Alapaha River Basin
Suwannee River
Hydrography
2.5 1.25 0
Miles
2.5
# Rainfall Stations
Figure 3-3. Locations of rainfall stations in the Alapaha River study area.
3-5
3.2.4 Permit Data
Water-use data are available by county from the District. These data provide information as to
the general locations of water users within the Florida portion of the Alapaha River Basin.
3.2.5 Summary
The data available for the determination of minimum flows and levels for the Alapaha Basin
include:
Excellent, continuous discharge and stage data for the Alapaha River near
Statenville, GA;
Spotty continuous stage and discharge data or the Alapaha River near Jennings;
Very limited discharge data from the Jasper gage and for the Alapaha Rise;
Quarterly, monthly, or bi-monthly groundwater level data from ten sites;
Daily measurements in two monitoring wells (USGS Ref. No. 02317500 and
02317620) provide ability to correlate ground- and surfacewater levels;
Groundwater permit information is available, by county in Florida;
Monthly rainfall data from several stations; and
Daily rainfall data from one station at Jasper.
Significant shortcomings of the available data include:
The gaps in long-term, stage and discharge data for some gages on the Alapaha
River;
The relatively few groundwater wells with any significant record; and
No data on actual water use.
3.3 Data Simulation and Analysis

3.3.1 Methods
3.3.1.1 Simulation of River Data
One of the major data needs for establishing the MFL for the Alapaha River is a long-term time
series of stage and discharge in Florida, above and below the river sinks. As discussed in
Section 3.1.1.1, there is a long time series for the gage on the Alapaha River at Statenville, GA,
though most of these stage data were not available in digital format. The Alapaha River near
Jennings, FL gage is located just upstream from the sinks. Data from the Jennings gage goes
back several decades; however data gaps exist. The Alapaha River near Jasper, FL gage is
located several miles downstream from the sinks; the river dries up at this location during low
flow conditions. Data from the Jasper gage is spotty, though they span several decades.
3-6
Data were simulated by developing linear regression equations that relate incomplete data sets
to more complete ones. For several of the gages, a stage-discharge rating was developed in
order to calculate discharge from stage or vice-versa. To accomplish this, the stage-discharge
curves were broken into several portions based on apparent inflection points in the curve. For
example, a linear regression may best describe the relationship between stage and discharge at
low flows, whereas a polynomial equation may be required to characterize the relationship
between the data at higher flows.
Regression equations were developed using either Excel or Systat. Excel was utilized for
simple regression calculations (Willis, 2004) between two variables and Systat was utilized for
multiple regression (Davis, 1986). Step-wise multiple regression methods (Davis, 1986) were
utilized where more than one independent variable (i.e., stage or discharge at a stream gage,
groundwater levels, or rainfall data) had a potential influence on the dependent variable (stage
or discharge data at the gage or measurement site of interest). Goodness of fit was determined
by calculation of the coefficient of determination.(squared multiple correlation coefficient or R2).
Note that regression using correlated data for the purposes of predicting a response or
identifying trends is discouraged because of data autocorrelation and possible over-
determination of the relationships between the correlated data. The use of gage data from
elsewhere in the Alapaha River drainage to estimate stage or flow data at a site with partial data
involves purposeful reliance on the auto-correlation properties of the data sets. In essence, the
regressions quantify the correlations in order to estimate behavior at the site where data are
lacking.
The regression equations were developed to characterize a set of historic hydrologic

phenomena. They were used to hindcast hydrologic behavior relationships between highly
correlated and controlled data. As such, the regressions should not be utilized to forecast future
events because the hydrologic system may change, and the forecast responses are
uncontrolled and un-testable.
3.3.1.2 Simulation of Alapaha Rise Discharge

The Alapaha Rise, first magnitude resurgent (spring), is on the Districts priority list for MFL
development. The Alapaha Rise MFL(s) will be developed as part of the upper Suwannee MFL
project and are not addressed in this report. Even so, estimating some partial or full period of
record for discharge from the Alapaha Rise is important for characterizing the behavior of
developing a MFL for the Alapaha River.
A time series of discharge data was simulated for the Alapaha Rise by conducting an analysis of
the relationships between river discharge, groundwater levels, and measured Alapaha Rise
discharge using step-wise multiple regression methods.
As will be seen, there was a significant time lag between river and groundwater events and
discharge responses at the resurgence. In order to incorporate the appropriate time lag into the
data simulation process, several cross-correlation (Davis, 1986) graphs were created using
Systat. Once the appropriate lag time was found, cross-plots of Alapaha Rise discharge (using
the 79 measured values; Table 3-2) versus the river or well data were created. Generating
trend lines for the data and evaluating various types of trends (e.g. linear, logarithmic,
polynomial) and the goodness of their fit produced simplified relationships between Alapaha
Rise discharge and the other variables. These relationships, or equations, relating Alapaha
Rise discharge to river and/or groundwater data were used to generate partial or full periods of
3-7
record (depending on whether the relationship can be extended to the full range of river or well
data) for Alapaha Rise discharge.
3.3.1.3 Uncertainty Associated With Data Simulation

The Alapaha River, Rise, and related portions of the Floridan Aquifer form a complex hydrologic
system. Due to this level of complexity, there is a level of uncertainty that goes along with
simulating data for the Alapaha River and Rise. The uncertainty results from a combination of
data dispersion about the regression equation lines and un-characterized complexities in the
hydrogeologic system.
This uncertainty is additive at each step in the data simulation process. Even if the uncertainty
associated with each step in the process of data simulation is kept to a minimum, by the time
the last step is reached, the uncertainty is compounded. As will be seen in the Section 3.3,
uncertainty is kept to a minimum during each phase of data simulation. Even so, the sequence
of simulations and the inherent complexities of the system result in some uncertainty,
particularly with the peak stage and discharge values, which are commonly somewhat under
estimated during simulation.
3.3.2 Alapaha River

Data were simulated for the gages located on the Alapaha River at Statenville, near Jennings,
and near Jasper. Data needs varied for these three gages; methods utilized for each gage were
targeted at these specific needs. These analyses allowed for the generation of over 70 years of
hydrologic data for the Alapaha River at these three gages.
3.3.2.1 Alapaha River at Statenville

The stream gage located on the Alapaha River at Statenville has been recording stage and
discharge data continuously since 1931. The discharge data for the full period of record have
been digitized; however, the corresponding stage data were only available beginning in 1997.
Therefore, a stage-discharge rating curve was developed to simulate the remaining, undigitized
stage data.
During the 70+ years the Statenville gage has been collecting data, the site has been visited on
an approximately monthly basis to obtain an actual measurement of the stage and discharge
through determination of the stream velocity and cross-sectional area. These data were cross-
plotted to generate a stage-discharge rating curve for this gage (Figure 3-4). The stage for each
corresponding daily value of discharge was then simulated using this rating curve.
3-8
30000
25000
20000
y = 3445.5x - 345405
Discharge (cfs)
R2 = 0.8541
15000
10000
y = 273.18x - 21394
R2 = 0.9843
5000
0
70 80 90 100 110
Stage (ft., NGVD)
Figure 3-4. Rating curve for the Alapaha River at Statenville, Georgia.
3-9
Figure 3-5 shows a comparison between observed and simulated daily values. Generally, the fit
of the simulated data to the measured is excellent, and the corresponding R2 value is 0.9991.
This process compensated for the lack of digital stage data and provided a continuous record of
both stage and discharge for the Alapaha River at Statenville extending back 70+ years.
110
1:1 Ratio
105
110
Simulated Stage (ft., NGVD)
100
Daily Value
95
Simulated
105 90
85
80
100 75
75 80 85 90 95 100 105 110
Measured Stage (ft., NGVD)
95
Stage (ft)
90
85
80
75
Oct-97 Oct-98 Oct-99 Oct-00 Oct-01 Oct-02 Oct-03
Date
Figure 3-5. Comparison of simulated and measured daily stage of the Alapaha River at
Statenville for 1997 through 2003. Inset compares the simulated and measured values to a 1:1
ratio line.
3-10
3.3.2.2 Alapaha River near Jennings
The stream gage located on the Alapaha River near Jennings was originally installed in 1976.
Data was continuously recorded, with short data gaps, until 1987 when the gage was
discontinued. In 1999, continuous data collection resumed.
A cross-plot of the stage data1 for the Statenville and Jennings gage indicated that these two
datasets are highly correlated (Figure 3-6). An exponential trend line resulted in the best fit to
the data, with an R2 value of 0.9815. This exponential equation was used to simulate stage
data for the Jennings gage back to 1931 (the period of record for the Statenville gage). A
comparison of the daily value stage data to the simulated data for a five-year period beginning
in 1999 is shown in Figure 3-7. The match is generally excellent, particularly at low stages, with
some of the flood peaks being moderately over or under estimated.
95
90
Alapaha River near Jennings, stage (ft)
85
y = 0.4811x1.1151
R2 = 0.9815
80
75
70
65
60
75 80 85 90 95 100 105 110
Alapaha River at Statenville, stage (ft)
Figure 3-6. Cross-plot of the stage of the Alapaha River at Statenville versus daily stage
measurements at the Jennings gage.
1
Whenever simulated and measured data exist for the same date, the measured data are utilized
throughout this report. Simulated data are inserted only to fill data gaps.
3-11
90
Daily Stage Values
Simulated Stage Values
85 95
Simulated stage at the Jennings gage (ft., NGVD)

1:1 Ratio
90
85
80
80
75
70
Stage (ft)
65
75 60
60 65 70 75 80 85 90 95
Measured Stage at the Jennings gage (ft., NGVD)
70
65
60
Oct-99 Oct-00 Oct-01 Oct-02 Oct-03
Date
Figure 3-7. Comparison of simulated and measured daily stage values for the Alapaha River at the
gage near Jennings for the period from 1999 to 2003. Inset compares the measured and simulated
stage data to a 1:1 ratio line.
A rating curve (Figure 3-8) was developed for the Jennings gage in order to simulate discharge
from the simulated stage data. A comparison of the daily value discharge data to the simulated
data for a five-year period beginning in 1999 is shown in Figure 3-9. Again, the match is
generally excellent, particularly at low stages, with some of the flood peaks being moderately
over or under estimated. This process allowed for the simulation of a 70+-year period of record
for the Jennings gage.
3-12
20,000
18,000
16,000
14,000 y = 1237.8x - 94307

R2 = 0.9297
Discharge (cfs)
12,000
10,000
8,000
y = 357.69x - 22134
6,000
R2 = 0.983
4,000
2,000
0
60 65 70 75 80 85 90 95
Stage (ft., NGVD)
Figure 3-8. Rating curve based on stage and discharge measurements at the Jennings gage.
3-13
90
90
Daily Stage Values 1:1 Ratio
Simulated Stage Values 85
Simulated Stage (ft., NGVD)

85 80
75
70
80
65
Stage (ft)
60
60 65 70 75 80 85 90
75 Measured Stage (ft., NGVD)
70
65
60
Oct-99 Oct-00 Oct-01 Oct-02 Oct-03
Date
Figure 3-9. Comparison of simulated and measured daily discharge from 1999 through 2003 for the Alapaha
River at the gage near Jennings. Inset compares the measured and simulated data to a 1:1 ratio line.
3-14
3.3.2.3 Alapaha River near Jasper
Of the three stream gages included in this study, the one located on the Alapaha River near
Jasper had the most incomplete data set. This gage was never continuously monitored.
Random measurements of stage and discharge exist back to the 1950s (Table 3-2), however.
As discussed in Section 2.3, the Dead River and swallets located within the Alapaha River
streambed between the Jennings and Jasper gages capture a portion of the stream flow.
During low-flow conditions, these sinks capture 100% of the discharge recorded at the Jennings
gage, resulting in a dry stream in the vicinity of the Jasper gage. Therefore, comparison of
historical stage data for these two gages is complex, particularly for low-flow conditions.
The long-term record of discharge at the Jasper gage is critical to understanding the role of the
swallets and conditions for river flow downstream of the swallets. This data set allows for an
assessment of the relative portion of stream flow that is captured by the sinks, as well as an
assessment of discharge frequencies within the river downstream from the swallets.
Figure 3-10 shows a cross-plot of the simulated1 discharge for the Jennings gage and the
available discharge measurements for the Jasper gage (including site visits when the discharge
at Jasper was zero) to demonstrate the response of the river to the swallet system that lies
between the two gages. Close inspection of this graph reveals three distinct trends within the
data. The first is within the data nearest the origin. Here, Jennings discharge increases while
Jasper discharge remains zero, resulting in a vertical trend line. At some point, the discharge
measured at the Jasper gage begins to increase above zero and a linear trend is observed in
the data from this point to a value of discharge at the Jennings gage of approximately 8,000 cfs.
Above this point on the graph, the data appear to be much more weakly correlated and do not
follow the previously mentioned trend.
The loss of correlation among the data at high discharge appears to be an artifact of the data
simulation process. As discussed above, the flood peaks were frequently over- or
underestimated in the simulated discharge data for the Jennings gage. These high discharge
data were, therefore, dropped from the analysis. The data corresponding to zero discharge at
Jasper were also dropped, and the remaining data show the relationship between flow at the
Jasper gage and flow at the Jennings gage (Figure 3-11).
3-15
14000
12000
Alapaha River near Jennings, discharge (cfs)
10000
8000
6000
4000
2000
0
0 5000 10000 15000 20000 25000 30000
Alapaha River near Jasper, discharge (cfs)
Figure 3-10. Cross-plot of simulated Alapaha River discharge near Jennings versus measured discharge of the Alapaha
near Jasper.
3-16
12000
10000
y = 1.2723x + 510.16
2
R = 0.9536
8000
6000
4000
2000
0
0 1000 2000 3000 4000 5000 6000 7000 8000
Figure 3-11. Cross-plot of discharge data from the Alapaha River at Jennings and Jasper. The graph excludes data when
flow at Jasper was zero and when it was greater than 8,000 cfs.
3-17
An excellent linear trend is observed in these data, with a Y-intercept at approximately 500 cfs.
Therefore, Dead River and the swallets within the streambed capture the first ~500 cfs of
discharge recorded at the Jennings gage and the discharge at Jennings must exceed ~500 cfs
before any stream flow will be observed at the Jasper gage. Furthermore, the slope of the trend
line indicates that, for any additional discharge beyond the 500 cfs threshold, approximately
80% of the flow will reach the Jasper gage. So the sinks within the Alapaha River capture the
first ~500 cfs of flow, plus about 20% of any additional flow. In other words, if discharge at
Jennings is less than 500 cfs, the reach of the river downstream from the swallets is dry. When
the discharge is greater than 500 cfs at Jennings, 500 cfs plus 20% of any discharge greater
than 500 cfs, enters the Floridan Aquifer via the swallet system and the remainder passes
downstream to the Jasper gage and beyond. For example, if discharge at Jennings is 1,000
cfs, then it is estimated that 600 cfs would be captured by the swallet system and 400 cfs would
pass downstream.
Figure 3-12 compares simulated and measured Jasper discharge data during the period from
1980 to 2000. Generally, the agreement between the data is excellent, particularly at low flows.
Some flood peaks appear to be underestimated (Inset, Figure 3-12). This process allowed for
the simulation of a 70+-year period of record of discharge for the Jasper gage.
16000
16000
14000
14000 12000
Simulated Discharge (cfs)
1:1 Ratio
10000
Discharge Measurements
8000
Simulated Daily Discharge
6000
12000
4000
2000
0
10000 0 2000 4000 6000 8000 10000 12000 14000 16000
Measured Discharge (cfs)
8000
6000
4000
2000
0
10/1/80 10/1/85 10/1/90 10/1/95 10/1/00
Date
Figure 3-12. Comparison of simulated daily discharge to measured discharge of the Alapaha River at
the gage near Jasper. Insert compares measured and simulated discharge to a 1:1 ratio line.
3-18
3.3.2.4 Summary of River Data Simulation
Through development of rating curves and the use of linear regression analysis the stage and
discharge data sequences for the gages on the Alapaha River at Statenville and near Jennings
have been filled in and extended, and a 70+ year period of record was developed. Linear
regression analysis also allowed for the simulation of 70+ years of discharge data for the gage
on the Alapaha River near Jasper. Stage data were not simulated for the Jasper gage.
The relationship between Jasper and Jennings discharge also indicates the amount of Alapaha
River flow recorded at Jennings that discharges into the groundwater system through swallets
located downstream of the Jennings gage.
3.3.3 Predicting Resurgence Discharge

As previously discussed, there is a loss of stream flow into the underlying aquifer through Dead
River and swallets within the stream bed just south (downstream) of the SR 150 bridge. During
low flows, (less than ~500 cfs at the Jennings gage), all of the stream flow is captured by these
swallets. Most, if not all, of this water travels through caverns and conduits within the aquifer,
and eventually discharges from resurgences (springs) along the Suwannee River.
By far, the largest resurgence is the Alapaha Rise (Figure 1-1b), which has measured discharge
that ranges from ~200 to ~1,100 cfs. Holton Creek Rise, located near the Alapaha Rise (Figure
1-1b), also apparently receives significant flow from captured Alapaha River water (Ceryak,
1977).
This section characterizes discharge relationships at the resurgences to Suwannee River flow.
MFLs will be developed for the resurgences when the MFLs for the upper Suwannee River
basin are developed. For the purposes of this report, the discharge characteristics of the
resurgences are discussed for context and as a reality check with respect to understanding the
fate of water captured in the Alapaha swallets.
3.3.3.1 Alapaha Rise
The Alapaha Rise is, by far, the largest of the Alapaha resurgences. The Alapaha Rise has
measured discharge that ranges from ~200 to ~1,100 cfs, so it is considered a first magnitude
spring.
Discharge from the Alapaha Rise consists of some portion of base flow from the aquifer as well
as the reemergence of captured stream flow. During extreme low flow conditions in the Alapaha
River, discharge from the Alapaha Rise exceeds stream flow measured at the Alapaha River
near Jennings. During extreme floods in the Alapaha River, the river discharge (and
corresponding portion captured by the sinks within the riverbed) can be significantly greater than
discharge at the Alapaha Rise. In such a complex system, a simple relationship between
upstream and downstream discharge (like that observed between the Statenville and Jennings
gages) is not expected.
Relationship of Alapaha Rise Discharge to the Alapaha River - Figure 3-13 shows a cross-
plot of simulated discharge of the Alapaha River near Jennings and measured discharge at the
Alapaha Rise. There are two distinct patterns within the data - the areas above and below a
discharge value of ~500 cfs at the Alapaha River near Jennings (vertical line on Figure 3-13).
Recall that the value of ~500 cfs is the threshold observed within the river below which all flow is
captured by the swallets. Recall also that, as flow exceeds 500 cfs, about 20% of the portion
exceeding 500 cfs is also captured.
3-19
1200
1000
800
Alapaha Rise, discharge (cfs)
600
400
200
500 cfs threshold
0
0 1000 2000 3000 4000 5000 6000 7000
Figure 3-13. Cross-plot of Alapaha Rise discharge measurements and simulated daily discharge of the Alapaha River near Jennings.
3-20
Figure 3-14 and 3-15 separate the data at this 500 cfs value. The data depicted in Figure 3-14,
which correspond to flow in the Alapaha River near Jennings less than 500 cfs, exhibit a weak
linear trend. During times when flow in the Alapaha River near Jennings exceeds 500 cfs,
Alapaha Rise discharge is apparently more-or-less unrelated to concurrent river discharge
(Figure 3-15).
Figure 3-16 depicts the cross-correlation coefficients between Alapaha Rise and Alapaha River
near Jennings data for time when the flow at Jennings was less than 500 cfs. As the arrow in
Figure 3-16 indicates, the maximum correlation coefficient is in the vicinity of 4 and 6 days
(highest correlation coefficient is at -6 days). A negative lag indicated that the discharge signal
at the Alapaha Rise is 4 to 6 days later than the discharge event at the Jennings gage.
While there is little to no relationship evident within either Figure 3-14 or 3-15, these graphs do
not take into account any lag that may be present between these data sets. It is likely that the
recharge signal to the aquifer from captured stream flow is significantly lagged relative to
discharge signal at the Alapaha Rise because of storage with the aquifer. As there appear to be
two distinct flow regimes within this system (discharge at the Alapaha River near Jennings
above and below ~500 cfs), the lag time may differ significantly between these flow regimes.
Figure 3-17 shows a cross-plot of the Jennings discharge data lagged 6 days (Figure 3-16)
versus measured discharge at the Alapaha Rise when river discharge is less than 500 cfs.
Comparison with Figure 3-14 indicates that a significantly better trend was observed when
incorporating this response time lag. For example, the R2 increased from 0.62 to 0.71 by
lagging the data.
Figure 3-18 is the cross-correlation graph comparing discharge at the Alapaha River near
Jennings greater than 500 cfs with measured discharge at the Alapaha Rise. The lag yielding
the best correlation coefficient is much greater than in Figure 3-16. The most significant
correlation between the data was when Jennings discharge was lagged 21 days (lag = -21
days) ahead of Alapaha Rise discharge. In this case, the difference between the lagged and
unlagged data is much more striking; a significant trend (R2 = 0.72) exists when using the
lagged data (Figure 3-19) whereas no trend was present using the unlagged data (R2 = 0.09;
Figure 3-15).
3-21
700
650
600
y = 0.799x + 275.81
2
R = 0.6171
550
Alapaha Rise. Discharge (cfs)
500
450
400
350
300
250
200
0 100 200 300 400 500 600
Figure 3-14. Cross-plot of discharge measurements from the Alapaha Rise with simulated daily discharge of the Alapaha River near
Jennings, when river discharge is <500 cfs.
3-22
1100
1000
900
y = 0.0311x + 584.01
2
R = 0.0928
800
700
600
500
400
0 1000 2000 3000 4000 5000 6000 7000
Figure 3-15. Cross-plot of Alapaha Rise discharge measurements and simulated, daily Alapaha River discharge near Jennings for days
when Jennings discharge was >500 cfs.
3-23
p g g
0.8
0.7
0.6
Corrolation Coefficient
0.5
0.4
0.3
0.2
0.1
0
-25 -20 -15 -10 -5 0 5 10 15 20 25
Lag (days)
Figure 3-16. Cross-correlation graph showing correlations of Alapaha Rise discharge measurements lagged against simulated
discharge of the Alapaha River at Jennings. Comparison is for times when Jennings discharge was less than 500 cfs only.
3-24
700
650
600
550
500
450
400
y = 0.6551x + 273.01
2
R = 0.7085
350
300
250
200
0 100 200 300 400 500 600
Alapaha River near Jennings, lagged discharge (cfs)
Figure 3-17. Cross-plot of Alapaha Rise discharge measurements versus discharge <500 cfs of the Alapaha River near Jennings lagged
6 days.
3-25
p g g
0.8
0.7
0.6
Corrolation Coefficient
0.5
0.4
0.3
0.2
0.1
0
-50 -45 -40 -35 -30 -25 -20 -15 -10 -5 0
Lag (days)
Figure 3-18. Cross-correlation graph comparing discharge measurements in the Alapaha Rise to simulated discharge >500 cfs
in the Alapaha River near Jennings. The arrow indicates the highest correlation at a lag of 21 days.
3-26
1200
1100
1000
900
800
y = 0.0757x + 487.28
2
R = 0.7223
700
600
500
400
0 1000 2000 3000 4000 5000 6000 7000
Alapaha River near Jennings, -21-day lagged discharge (cfs)
Figure 3-19. Cross-plot of Alapaha Rise discharge measurements and -21-day lagged discharge >500 cfs in the Alapaha
River near Jennings.
3-27
The difference in lag times between the two flow regimes is most likely related to the hydrologic
system and its ability to transmit flow from the river sinks to the Alapaha Rise. During low flow,
the caverns and conduits that convey water from the sinks to the rise can efficiently transfer the
input from the river although a time lag on the order of one week is required for the signal to be
transmitted. During high flows, however, the systems ability to transmit water is overwhelmed,
and much of the water that flows into the sinks is taken up by the aquifer as storage. This water
is then released more gradually, resulting in the longer lag time, on the order of several weeks.
While incorporating a lag between river and Alapaha Rise discharge events clearly increases
the correlation between these data, the observed trend is still relatively weak (R2 values
between 0.7 and 0.73). This is likely due to a combination of factors, and reflects the complexity
of this system. Factors that may affect Alapaha Rise discharge other than the input from the
river include:
Long-term water levels in the aquifer (i.e. drought versus wetter periods);
Other local recharge (e.g. precipitation falling on the unconfined portion of the Floridan
Aquifer within the area contributing to Alapaha Rise discharge);
The stage of the Suwannee River, which receives Alapaha Rise discharge (higher river
stages may inhibit spring discharge); and
Aliasing of cyclic discharge events in the Alapaha Rise, which may result in an
incomplete match between Alapaha River and Alapaha Rise discharge events.
These possible causes are explored further below.
Relationship of Alapaha Rise Discharge and Aquifer Levels - Floridan Aquifer water levels
in the vicinity of Alapaha Rise fluctuate due to several processes. Water is recharged to the
Floridan Aquifer as stream flow in the Alapaha River is captured by sinks and swallets located
within the streambed. The Floridan Aquifer is unconfined in the vicinity of the Alapaha Rise;
local rainfall directly recharges the aquifer in this area. Discharge from the aquifer occurs as
water flows from springs and as base flow directly to the Suwannee River.
As discussed above, Alapaha Rise discharge is weakly related to lagged Alapaha River
discharge, measured upstream from the sinks and swallets found in the streambed. Floridan
Aquifer levels depend on recharge from the river and from local rainfall, so a comparison
between aquifer levels and Alapaha Rise discharge would account for both of these processes.
This analysis also accounts for the affect of long-term hydrologic conditions on aquifer
discharge.
Several wells with a significantly long period of continuous monitoring are located within the
study area. Of these, Well #10 (Figure 3-1) has the longest period of record, with continuous
monitoring beginning around 1980. Figure 3-20 is the cross-correlation plot corresponding to
Alapaha Rise discharge and water level measurements for Well #10. The peak in the plot (R2 =
0.91) is located at a lag of -2 days, indicating the discharge at Alapaha Rise is most related to
water levels in Well #10 measured two days earlier.
3-28
0.95
0.93
0.91
0.89
Correlation Coefficient
0.87
0.85
0.83
0.81
0.79
0.77
0.75
-15 -10 -5 0 5 10 15
Lag (days)
Figure 3-20. Cross-correlation graph comparing Alapaha Rise discharge measurements and water levels in Well #10. Arrow
indicates the lag with the highest correlation coefficient.
3-29
Since the Alapaha Rise is a resurgence with a groundwater contribution, it is important to
understand the relationship of resurgence discharge and groundwater levels. Figure 3-21
shows a cross-plot of Alapaha Rise discharge versus the lagged water level in Well #10. The
trend line shows a logarithmic relationship between the data. Using this relationship, the
discharge at Alapaha Rise was simulated for the ~20 year period within which data were
available for Well #10. The predicted discharge is shown in Figure 3-22, along with the flow
measurements for comparison.
Relationship of Rise Discharge and Suwannee River Stage - The Alapaha Rise is located on
the northern bank of the Suwannee River. Therefore, the water level within the spring reflects
the stage within the Suwannee River in the vicinity of the Alapaha Rise as well as the potential
of groundwater flowing out of the spring. During high discharge events within the Suwannee
River, the stage within the Rise increases as river stage increases. As river stage drops,
discharge from the Rise should increase, all else being equal. This section examines what
effect, if any, the river stage has on the discharge from the Alapaha Rise.
Smaller streams in karst terrains often experience backwater and hysteresis effects in the
vicinity of the larger stream to which they discharge during flood events. The backwater effect is
caused by high stage in the larger river inhibiting discharge during flood. The hysteresis effect
is caused by bank, channel, and floodplain storage and, in karst terrains, the estavelle action of
springs that reverse flow and become aquifer recharge points during floods.
This backwater/hysteresis effect results in a looped appearance to the stage-discharge graph

for gages on the smaller stream in the vicinity of the confluence with the larger stream. This
phenomenon is common on the nearby Withlacoochee River, with the effect realized as far
upstream as the gage at Pinetta (located ~20 miles upstream from confluence with the
Suwannee River) during very large floods on the Suwannee River (WRA, 2005). The
consequence of this phenomenon is that, for a given stage in the tributary river, the discharge
will decline during rising stage and increase during falling stage.
A graph of stage versus discharge for the Alapaha Rise would exhibit the pattern described
above if stage in the Suwannee River exerts a significant control over discharge from the Rise.
As discussed in the previous section, an approximately 20-year period of record of discharge
has been simulated for the Alapaha Rise. However, no daily values are available for stage
within the Rise itself. The gage on the Suwannee River at Ellaville, which has been recording
data for almost 80 years, is a few miles downstream from the Alapaha Rise. Stage at the
Ellaville gage is affected by discharge from the Alapaha and Withlacoochee Rivers, as well as,
channel and bank storage/estavelle action in the Suwannee River. While stage at this gage is
obviously somewhat less than stage within the Alapaha Rise itself and there are extraneous
causes of stage variations at Ellaville, the pattern of stage at the Ellaville gage and within the
Rise are likely similar.
Using the stage data from the gage on the Suwannee River at Ellaville as a proxy for stage
within the Alapaha Rise, a stage-discharge plot was constructed using the simulated discharge
data for the spring (Figure 3-23). This plot clearly shows a looped pattern. However, as
illustrated by close examination of a single flood event, this pattern is different from the pattern
described above. Normally, the discharge should diminish as stage in the receiving water (the
Suwannee River) increases. As stage declines, the discharge should then increase.
3-30
1100
1000
900
800
Alapaha Rise Q (cfs)
y = 1358.8Ln(x) - 4552.9
R2 = 0.9104
700
600
500
400
300
200
30 35 40 45 50 55
Lagged Well #10 head (ft)
Figure 3-21. Cross-plot of Alapaha Rise discharge with water levels in Well #10 lagged 2 days ahead of discharge from the resurgence
(lag = -2 days).
3-31
1200
Measured Discharge
Simulated Daily Discharge
1100
1200
1000
1000
Sim ulated Discharge (cfs)

800
1:1 Ratio Line
600
900
400
200
800 0
0 200 400 600 800 1000 1200
Measured Discharge (cfs)
700
600
500
400
300
200
1/1/81 1/1/84 1/1/87 1/1/90 1/1/93 1/1/96 1/1/99 1/1/02
Date
Figure 3-22. Comparison of daily discharge from the Alapaha Rise as simulated from lagged water levels in Well #10 with
measured resurgence discharge.
3-32
65
60
55
Suwannee River at Ellaville, stage (ft)
50
45
40
35
30
25
200 300 400 500 600 700 800 900 1000 1100 1200
Figure 3-23. Cross-plot of Suwannee River stage at the Ellaville gage with simulated Alapaha Rise discharge.
3-33
Figure 3-24 shows the portion of Figure 3-23 that corresponds to February and March of 1986.
The arrows, showing the direction of time, clearly illustrate that discharge from the Rise
increased as stage in the river increased. Peak discharge at the Rise occurred as the stage in
the Suwannee reached a maximum. Peak discharge then continued as stage in the river
declined. If this looping pattern were due to a backwatering effect created by the stage in the
Suwannee River, discharge should have been greatest during falling river stage. In this case,
discharge for a given level of stage is less during rising stage than it is during falling stage. This
scenario is consistent with the lag times experienced by flood pulses as they are initially taken
up by the Floridan Aquifer and released through the Alapaha Rise over time. In fact, the circled
data point on Figure 3-23 indicates the date of peak discharge in the Alapaha River and the time
of maximum loss from the river to the swallets. This peak was approximately two weeks prior to
peak discharge from the Alapaha Rise.
Estavelle Action of the Alapaha Rise There is no evidence that the stage of the Suwannee
River has been high enough to force reversal of flow in the Alapaha Rise. Given the magnitude
of flow from the resurgence, it is probable that high river levels would reduce discharge,
however. Based on the example shown in Figure 3-23, it appears that flooding of the Alapaha
creates sufficient head in the Floridan Aquifer that discharge from the resurgence can counter
act much of the potential head reversal in the Rise.
The stage of the Suwannee River controls the stage within the Alapaha Rise. Therefore, some
effect on the Alapaha Rise discharge due to fluctuations in river stage must exist. However, the
preceding example clearly shows that this effect is small (and therefore unapparent) compared
to the large effect of the lag time between peak discharge into the sinks within the streambed
and the peak discharge from the Alapaha Rise. This lag, due to incorporation of stream flow
into Floridan Aquifer storage, which is then slowly released over time, creates a uniquely
looping stage-discharge curve for the Alapaha Rise.
Aliasing - Aliasing is a statistical term relating to the frequency of sampling of cyclic data
(Davis, 1986; Upchurch et al., 2005). If the interval between data collection events is longer
than the period, or time interval between successive peaks or valleys in the cyclic time series,
then the cycles cannot be identified and there is a risk that any trends in the data are a result of
the timing of sampling and not of a true trend. If the sampling interval coincides with the period
of the cycle, a trend will not be detected because all samples will fall on the same portion of the
cycle. If the sampling interval is less than the period of the cycle, then the cycle may be partially
or fully characterized by the data.
There was a concern that the periodic sampling of the Alapaha Rise may have resulted in an
aliased data set. Had the data been aliased, the cross-correlations (Figures 3-16, 3-18, and 3-
20) would not have worked. The lag times would not have been hydrologically realistic and the
occurrence of the lags just prior to the discharge events would not have been evident.
Therefore, it appears that aliasing is not a serious problem and that the cross-correlation data
and lag times used for regression modeling are appropriate.
Summary of Alapaha Rise Discharge Relationships - The contemporaneous discharge data

for the Alapaha River near Jennings and the Alapaha Rise display a weak relationship during
low flows (Jennings discharge less than 500 cfs) and no relationship during high flows (Jennings
discharge greater than 500 cfs). Cross-correlation analysis of these data indicate the maximum
correlation is found when Alapaha Rise discharge is lagged 6 and 21 days behind the Alapaha
River near Jennings discharge for the low and high flow data, respectively. An even better
3-34
relationship is found between Alapaha Rise discharge data and the water level data for Well
#10. Using this last relationship, a ~20 year period of record was simulated for the Alapaha
Rise.
An analysis of the relationships between Alapaha Rise discharge and Suwannee River stage
indicates that high water in the Suwannee River has minimal effect on discharge from Alapaha
Rise due to storage in the aquifer, the long lag times inherent to this system, and the magnitude
of the resurgence. At best, it appears that discharge from the Rise is inhibited during high stage
events in the Suwannee.
3-35
65
60
Suwannee River at Ellaville, stage (ft., NGVD)
55
50
45
40
35
750 800 850 900 950 1000 1050 1100
Figure 3-24. Cross-plot of stage of the Suwannee River at Ellaville versus simulated discharge from the Alapaha Rise for February
and March, 1986. The arrows indicate the direction of time, and the circled data point corresponds to the peak flow into the
swallets in the Alapaha River.
3-36
3.3.3.2 Holton Creek Rise
Holton Creek Rise, located near Alapaha Rise (Figure 1-1b), apparently also receives significant
flow from captured Alapaha River water (Ceryak, 1977). Only a handful of discharge
measurements, ranging from 0 to ~500 cfs, are available for this spring. Thus, simulation of
discharge from Holton Creek Rise is not possible.
There are three measurements of discharge from Holton Creek Rise during the period for which
simulated Alapaha Rise discharge data are available (Figure 3-25). While so few
measurements do not allow for a quantitative relational assessment of discharge, a more
qualitative assessment is possible. Flow from the Alapaha Rise has apparently not ceased in
the recent past (Figure 3-22). However, it appears that flow from the Holton Creek Rise ceases
during times of low Alapaha Rise discharge (< ~300 cfs at Alapaha Rise). As discharge
increases at Alapaha Rise, Holton Creek Rise begins to flow, but a large increase in discharge
at Alapaha Rise is accompanied by only a small increase in discharge at Holton Creek Rise.
Discharge from Holton Creek Rise is a larger percentage of Alapaha Rise discharge as flow
from the two springs increase. In this way, Holton Creek Rise appears to function like an
overflow valve for the Alapaha Rise, discharging a proportionally greater amount as Alapaha
Rise discharge increases.
By plotting the average Alapaha Rise discharge (545 cfs) on Figure 3-23, a qualitative
assessment of the average discharge at Holton Creek Rise can be made. Based on these
limited data, it would appear the average discharge at Holton Creek Rise is ~90 cfs. This
translates to a total average discharge from Alapaha and Holton Creek Rise of ~635 cfs.
Therefore, flow into the Alapaha River swallets accounts for, on average, ~80% of the discharge
from these springs, and only ~20% of the discharge, or about 125 cfs on average, is pickup to
the system from the Floridan Aquifer. Despite this, the relationship between appropriately
lagged Alapaha River and Rise discharge is moderately significant at best. Prevailing
hydrologic conditions (i.e. drought versus wetter periods) and/or other factors apparently have a
significant effect on the discharge to Alapaha Rise.
3.3.4 Discussion
The preceding analyses reveal a complex and intriguing hydrologic system with two distinct flow
regimes. Figure 3-26 illustrates the historic flow duration curve for the Alapaha River at
Jennings. The gage at Jennings is above the reach of the river where flow is captured by
swallets and the flow duration curve is uncomplicated. The flow duration curve for the Alapaha
River at Jasper (Figure 3-27) exhibits the added complication of zero flows over a significant
proportion of the time. When discharge is below ~500 cfs in the Alapaha River near Jennings,
all of the flow is diverted underground through sinks located within the river or through Dead
River. During these low flow periods, a pulse of water is transmitted through the Floridan
aquifer to the Alapaha Rise in approximately one week. That is to say, peak low or high
discharge from the Rise occurs about one week after occurring at the Jennings gage. When
discharge at the Jennings gage exceeds ~500 cfs, only a portion (~20%) of the flow exceeding
500 cfs is captured by the swallets and transmitted through the aquifer. During these high flow
periods, a flood pulse takes, on average, about three times longer to travel through the aquifer
to the Rise.
3-37
800
Average Holton Creek Discharge ~ 90 cfs?
700
Alapaha Rise simulated discharge (cfs)
600
Average Alapaha Rise Discharge = 545 cfs
500
400
300
200
0 20 40 60 80 100 120 140 160 180
Holton Creek Rise measured discharge (cfs)
Figure 3-25. Comparison of measured discharge from Holton Rise and Creek to simulated discharge from the Alapaha Rise.
3-38
100000
10000
1000
100
10
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Figure 3-26. Historic flow duration curve of the Alapaha River near Jennings. Abrupt offsets in the curve are a result of the
data simulation process.
3-39
10000
1000
Discharge (cfs)
Flow to Sinks Alapaha River near Jennings
100
Alapaha River near Jasper
10
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Figure 3-27. Comparison of the flow duration curves for the Alapaha River at Jasper and at Jennings. The FDC for the flow into
the swallets is shown as part of the Jennings FDC.
3-40
Figure 3-28 shows FDCs for the Alapaha Rise and for flow to the sinks for the period from
October 1, 1981 September 30, 2003 (the simulated period of record for the Rise). The FDCs
for the Alapaha River at Jennings and Jasper are based on measured or simulated data, as
discussed above. The FDC for flow to the swallets is the difference between the two river
FDCs. At flows less than 500 cfs, the FDC for flow to the sinks is the Jennings FDC because all
water in the river is captured by the swallets. At flow greater than 500 cfs, the difference
between the Jennings and Jasper FDCs is assumed to be that proportion of the water that
passes the Jennings gage but not the Jasper gage.
This graph (Figure 3-27) shows that discharge from the rise is greater than flow into the sinks
above an exceedance probability of ~50%. The discharge from the Rise more or less equals
the flow to the sinks for the range of exceedance probabilities between ~25 50%. Below an
exceedance probability of ~25% the flow to the sinks is greater than the discharge from Alapaha
Rise. Based on this, it is reasonable to assume that the system is gaining water from the
aquifer between the sinks and the Rise. In fact, the average simulated discharge to the Rise for
the 22 year period indicated above is 545 cfs, while the average flow to the sinks for the same
period is 510 cfs, indicating a groundwater pickup of ~7%.
This analysis neglects the contribution of the Alapaha River to flow from Holton Creek Rise,
however. It is apparent that the flow from Holton Creek Rise is a predominantly overflow from
the water being transported to the Alapaha Rise.
3-41
10000
Flow to Sinks
Alapaha Rise
1000
Discharge (cfs)
100
10
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Figure 3-28. Comparison of the FDCs for flow to the swallets in the Alapaha River and the Alapaha Rise.
Abrupt offsets in the FDCs are a result of the simulation process.
3-42
3.4 HEC-RAS Model for the Alapaha River
A transient and steady state HEC-RAS model was developed for the Alapaha River in order to
support ecological modeling of the river and MFL development. An existing steady state HEC-2
model of the Suwannee River including the Alapaha River was previously developed for flood
plain mapping (USACOE, 1989). The HEC-2 model was converted to HEC-RAS by Taylor
Engineering (Taylor Engineering, 2002). This converted model was again modified as
described below adding the transient simulation and additional surveyed cross sections as well
as better representing the low flow conditions through calibration. The text below describes the
tasks performed on the model simulating the Alapaha River Figure 3-29 shows the model
domain, simulated river cross sections, and observed gage locations.
22
. 63
21
. 48
ALAPAHA RIVER NEAR JENNINGS
3
!(
.9
19
CONFLUENCE OF ALAPAHA AND DEAD RIVER
5
!(
.
17
. 55
16
.5 2
15
13.27
11.92
ALAPAHA RIVER NEAR JASPER

!( 11.
2 1
10.01
9.10
7.5
1
6.62
5.2
6
4.15
2.7
6
2.06
135
. 52
140.18
141.11
133.96
SUWANNEE RIVER AT NOBLES FERRY

!( !( . 13
ALAPAHA RISE 137
Figure 3-29. Model domain, simulated river cross sections, and observed gage locations.
3-43
3.4.1 Model Data Development
A relational database was developed to store the observed flow and stage data for the Alapaha
River. The database was used to process the model input or boundary conditions as well as the
model calibration targets. Various tools were programmed into the database to assist in the
data management as well as processing the data into the requisite model input. All time series
data were then exported to the DSS format for use in the HEC-RAS model.
3.4.1.1 Model Boundary conditions

The model input time series or boundary conditions were stored and processed in a Microsoft
Access database. The processing included regressions to fill missing data (as discussed in
the previous section) and calculations to develop the downstream stage boundary. The time
series data was then transferred to the DSS format using DSSUTIL. Two types of boundary
conditions were used; stage boundary at the downstream end of the model domain and flow
boundary at the most upstream point, no lateral inflows (uniform nor point inflows) were included
in the model.
Boundary data are required to be continuous and complete for successful application in HEC-
RAS. Any missing periods in the observed data need to be filled prior to use in pickup
calculation and/or direct application in HEC-RAS. The Alapaha River near Jennings was
missing data from October 1997 to October 1998. Since the model time period is from October
1997 to September 2003, it was necessary to backfill Jennings discharge data to use the station
as an upstream boundary condition in the HEC-RAS model. The Jennings time series was filled
by using regression from surrounding discharge stations (as described in section 3.3.2.2)
The downstream stage boundary used in the Alapaha Calibration and predictive models were
simulated stages from the Suwannee River HEC-RAS Model. The observed and simulated
stages (as well as simulated flow) for the Nobles Ferry gage are shown in figure 3-30. The
Nobles Ferry gage is just upstream of the Alapaha confluence with the Suwannee River. The
simulated data is continuous with out data gaps while the observed data is sparse. The
simulated data was used directly to drive the Alapaha boundary rather than attempting to fit the
observed data with statistical techniques.
All boundary condition time series were stored as separate paths in the Boundary.DSS file. All
boundary data was recorded in the native daily time step. The DSS file contains 3 time series:
stage at Alapaha Rise, stage at confluence of Alapaha and Suwannee River and Flow at
Jennings.
3-44
Figure 3-30. Stage and flows at the Nobles Ferry gage.
3.4.1.2 Model Calibration data
Calibration data consists of all stage and flow data available within the model domain. The
stage comparisons are used to calibrate and verify the simulated frictions factors within the
model domain. Calibration data was available for Alapaha River near Jennings at RM 19.93
and Alapaha River near Jasper at RM 11.16. The stage and flow data for the calibration
stations were stored in an Access database. The data was then exported into HEC-RAS DSS
files.
3.4.2 HEC-RAS Model Development
As stated earlier, a HEC-RAS model was available for the Alapaha River. The original model
was developed for flood mapping. Models developed for flood mapping purposes are not
calibrated for low flow conditions. HEC-RAS is able to accurately simulate any type of river
system, however significant work was necessary to re-calibrate the existing model to better
represent the low flow conditions. Additional survey data was collected to help improve the low
flow calibration. Model stability at extreme low flow, especially when the river naturally runs dry,
is also an issue for numerical modeling. Additional model stability issues were addressed by
adding interpolated cross sections and pilot channel. The 25 interpolated cross-sections are
denoted by an * appended to the end of river mile in figure 3-31 shown below. Lastly it was
necessary to produce a transient and steady state models in order to calibrate to various flow
conditions and perform the ecological modeling.
3-45
Figure 3-31. River layout showing interpolated cross-sections.
The Alapaha River just downstream of confluence of Dead River is dry for most of the year
except during high flood events (>500 cfs at the Jennings gauge). A majority of flow in the
Alapaha River goes underground into karst formations. Much of this underground flow
reappears at Alapaha Rise just upstream of the confluence of Alapaha and Suwannee River.
To describe this occurrence in the numerical models, an underground segment was added. The
Alapaha River was then represented with three segments: upstream Alapaha River,
downstream Alapaha above ground, and downstream Alapaha below ground (karst conduit).
The upper segment stretches from the Alapaha at Jennings USGS Flow gauge to the
confluence with Dead River. The lower portion of the river is represented by two reaches one
simulating the overland portion from Dead River to the Suwannee River, the other representing
the underground karst conduit from the Dead River confluence flowing directly to the Suwannee
River representing the Alapaha River Rise and Holton Creek Rise. The water that enters the
sink on the Dead River run has been documented to exit at both the Alapaha River Rise and the
Holton Creek Rise which are relatively close to each other (as well as close to the Alapaha and
Suwannee River confluence). The flow in the Alapaha is allowed to discharge to both the above
ground and below ground segments. This represents this divergence of the Alapaha River as it
is split into Alapaha-above ground and Alapaha-below ground at RM 18.5.
Two shoals were surveyed to support this model development. Shoal information obtained was
at the confluence of the Alapaha and Dead Rivers at RM 18.5 and 18.48. The survey data
consists of cross sections in the Dead River near the confluence with the Alapaha River and just
3-46
upstream and down stream of the Dead River confluence in the Alapaha River. Another un-
surveyed shoal was added at RM 18.44. This added shoal was adjusted in order to calibrate
the stages at the Jennings Gage. This additional section also helped force water into the sink in
the Dead River. The additional section replicated the section at RM 18.48 while only modifying
the channel elevation 3 feet above RM 18.48. This shoal elevation also tremendously helped
stage calibration of Alapaha River near Jasper gage at RM 11.16. The physical presence of the
additional shoal was documented by personal communications. The elevation of the additional
shoal was adjusted to improve the calibration. The adjustments were made to improve the
flows and stages at the Alapaha near Jasper gauge. This gauge was sensitive to the additional
shoal elevation since the shoal controlled the occurrence and magnitude of the flows making it
to the Jasper station. All surveyed shoals were added to the HEC-RAS model. Figure 3-32
depicts the river profile with the added shoals highlighted.
Combined Suwannee System Plan: Plan 13 7/30/2006

Alapahaabove M ain Alapaha Main
100
Legend
Ground
90
80
Shoals at
70 Dead River
Deer
Elevation (ft)
Shoals
60 JUST UPSTREAM OF ALAPAHOOCHEE JUNCTION
50
SR-6 (41) BRIDGE NEAR JASPER
RR BRIDGE NEAR JENNINGS
NEAR FLA./GA. STATE LINE
40
INTERSTATE 75 BRIDGE
30
Jennings
20
0 20000 40000 60000 80000 100000 120000
Main Chan nel Distan ce (ft)
Figure 3-32. River profile with added shoals highlighted.
3-47
Combined Suwannee System Plan: Plan 13 7/30/2006
Alapahaabove M ain Alapaha Main
70 Legend
Ground
65
Elevation (ft)
60
JUST DOWNSTREAM OF ALAPAHOOCHEE JUNCTION
JUST UPSTREAM OF ALAPAHOOCHEE JUNCTION

55
RR BRIDGE NEAR JENNINGS

Added cross-section
Sill = 3 ft above the
previous
50
Jennings
85000 90000 95000 100000 105000 110000
Main Chan nel Distan ce (ft)
Figure 3-33. Shoal at RM 18.44 with elevation 3 above new shoal cross sections at RM
18.5 and RM 18.48.
The additional survey data was only available for the channel portion of the cross section.
Since the model extends into the floodplain, the surveyed cross sections were extended.
Extending the cross sections was accomplished by copying the closest available cross section
to the location of the surveyed section. The channel data was then replaced with the new
survey data. Since the focus of this study is to calibrate to the low flow conditions. The
floodplain is an area of lesser concern. The added cross-sections are fairly close to existing
cross-sections so the variability in the results will be negligible.
Since the Alapaha River goes dry downstream of Dead River, a pilot channel was necessary. A
pilot channel is merely a channel cross section modification for all sections defined for a river
segment. The modification is typically a narrow notch that extends below the bed. The pilot
channel is only active when the model runs dry and does not dramatically impact the model
results. A Pilot channel in the above ground section of the lower Alapaha was set to a width of
1 foot and a Mannings n of 0.07 with the slope determined by HEC-RAS. HEC-RAS
interpolates the data across all the cross sections between the specified end point cross
sections. For the Alapaha River, a pilot channel was added between RM 18.5 to RM 1.66 for
model stability. The pilot channel is only active during low flow conditions when the water
surface falls below the channel bed. Additional model stability issues were addressed by
adding interpolated cross sections and adding ineffective flow areas at bridges and other
appropriate cross-sections.
3-48
The processed model boundary conditions are listed below:
Upstream Boundary at RM 22.63 Alapaha River near Jennings Flow
Downstream Boundary for Alapaha-above ground at RM 1.66 Stages at confluence of
Alapaha and Suwannee River
Downstream Boundary at RM 1.66 for Alapaha-below ground Stages at Alapaha Rise
The model was constructed to simulate the six year period between 10/1/1997 to 9/29/2003.
This period included two significant wet periods and a severe drought. Confidence in the model
and its predictive capability is gained especially over the full range of flows included in the
simulation period. The computational time step of the model was set to 30 seconds. The
completed transient model takes approximately 2.5 hours to run on a 3.3 GHz Pentium class
machine.
3.4.2.1 HEC-RAS Model Calibration
The HEC-RAS model of the Alapaha River was calibrated by adjusting the channel elevation for
the shoal at RM 18.44 and the channel Mannings n friction factor. Consistency in the friction
factors was maintained in order to avoid point calibration and increasing the models predictive
capability. Table 3-4 shows the Mannings n used at each channel and river bank cross-section.
The calibration comparisons occur at gage locations where observed river stages are available.
Figures 3-34 and 3-35 show the calibration comparisons.
3-49
Table 3-4. Mannings n used at various cross-sections.
River Reach River Station Friction (n) Left Bank Channel Right Bank River Reach River Station Friction (n) Left Bank Channel Right Bank
1 Alapaha Main 22.63 n 0.3 0.05 0.3 67 Alapahaabove Main 11.7425* n 0.3 0.07 0.3
2 Alapaha Main 22.456* n 0.3 0.05 0.3 68 Alapahaabove Main 11.565* n 0.3 0.07 0.3
4 Alapaha Main 22.108* n 0.3 0.05 0.3 70 Alapahaabove Main 11.21 n 0.3 0.07 0.3
8 Alapaha Main 21.72 n 0.3 0.05 0.3 74 Alapahaabove Main 11.17 n 0.3 0.07 0.3
9 Alapaha Main 21.66* n 0.3 0.05 0.3 75 Alapahaabove Main 11.165 Bridge
34 Alapaha Main 18.98* n 0.3 0.05 0.3 100 Alapahaabove Main 8.05 Bridge
41 Alapahaabove Main 18.48 n 0.3 0.07 0.3 107 Alapahaabove Main 6.8425* n 0.3 0.07 0.3
42 Alapahaabove Main 18.44 n 0.3 0.07 0.3 108 Alapahaabove Main 6.62 n 0.3 0.07 0.3
43 Alapahaabove Main 18.385* n 0.3 0.07 0.3 109 Alapahaabove Main 6.28* n 0.3 0.07 0.3
50 Alapahaabove Main 17.1833* n 0.3 0.07 0.3 116 Alapahaabove Main 4.15 n 0.3 0.07 0.3
63 Alapahaabove Main 12.9325* n 0.3 0.07 0.3 129 Alapahabelow Main 18.48 n 0.3 0.008 0.3
66 Alapahaabove Main 11.92 n 0.3 0.07 0.3
3-50
Plan: Plan 13 River: Alapaha Reach: Main RS: 19.93
80 Legend
Stage
Obs Stage
Missing Data
75
Stage (ft)
70
65
Dec Mar Jun Sep Dec Mar Jun Sep

1999 2000 2001
Time
Figure 3-34. Calibration at Alapaha River near Jennings (Flow Boundary condition).
3-51
Plan: Plan 13 River: Alapahaabove Reach: Main RS: 11.16
75
Legend
Stage
Obs Stage
70
Missing Data
65
Stage (ft)
60
55
50
45
Apr Oct Apr Oct Apr Oct Apr Oct Apr Oct Apr
1998 1999 2000 2001 2002 2003
Time
Figure 3-35. Calibration at Alapaha River Near Jasper.
3.4.2.2 Exported HEC-RAS Data for EFM
Detailed output from HEC-RAS was exported to an ASCII file for use in the ecological modeling
of the Upper Santa Fe River. The detailed output defines the velocities, depths, wetted
perimeter, and other hydraulic properties for each cross section. This data was generated for
every 5th percentile from the observed flow and stage conditions. Each of the 5 percentile flow
and stage conditions was run in steady state within HEC-RAS. The detail output for each
steady state run was exported to an ASCII output file. The steady state output was exported to
define the horizontal velocity distribution. The detailed output is used to map the area of
preferred habitat for various species.
3-52
Combined Suw annee System Plan: Plan 13 6/27/2007
Alapahaabove M ai n Alapaha Mai n
Alapahabel ow Mai n
100 Legend
EG 01OCT 2000 0100

WS 01OCT 2000 0100
Cri t 01OCT 2000 0100
Ground
OWS 01OCT 2000 0100
80
Elevation (ft)
60
40
20
0 20000 40000 60000 80000 100000 120000
Mai n Channel Distance (ft)
Figure 3-36. Water level profile at low stage.
3.5 Use of the Discharge Data for MFL Development
The FDC for Jennings (Figure 3-26) is the best data set for MFL consideration because the data
are more nearly complete and synthesis of data to fill data gaps was minimal. It is
recommended that this FDC be considered as the historic FDC for MFL implementation and
permitting. Table 3-5 summarizes the population descriptors for the Alapaha River at Jennings
data for use in MFL development.
Table 3-5. Population Descriptors for Hydrologic Data from the Alapaha River at Jennings.
Population Descriptor Stage (feet, NGVD) Discharge (cfs)
Minimum 61.4 34.0
25th Percentile 62.2 137.5
Median (50th percentile) 63.5 477.0
75th Percentile 66.8 1,667.9
Maximum 90.1 18,122.9
Mean 65.8 1,403.9
Standard Deviation 5.5 2,170.8
Number of Data Points 5,214 5,539
Duration of Data 7/1979 9/2003 7/1976 9/2003
3-53
3.6 Temporal Variability of Hydrologic Conditions in the Alapaha River
The timing of high and low flows in the Alapaha River is important for consideration of ecological
issues. Box and whisker graphs were constructed to depict monthly variations in the Alapaha
River.
Figure 3-37 illustrates the stage and discharge variability of the Alapaha River at the Statenville,
Georgia gage. The simulated stage and discharge data from the Jennings gage (Figure 3-38)
and simulated discharge data Jasper gage (Figure 3-39) illustrate similar temporal patterns.
The monthly variation in discharge at the Alapaha Rise is depicted in Figure 3-39.
Note that the normal period of high discharge and stage occurs on all data sets from February
through April. Low flow occurs from June through November. The Jasper data clearly illustrate
the periods when the river below the swallets is typically dry (June through November). Lowest
discharge at the Alapaha Rise is typically in November (Figure 3-40) and highest discharge is in
March and April.
3-54
A
105
Q75 Max
100 Median Mini
Q25
Stage (ft. NGVD)
95
90
85
80
75
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
B
10000
9000
Q75 Max
8000 Median Mini
7000 Q25
Discharge (cfs)
6000
5000
4000
3000
2000
1000
0
Figure 3-37. Box and whisker diagrams showing the monthly variations in
stage (A) and discharge (B) at the Statenville gage.
3-55
A
85
Q75 Max
80 Median Mini
Q25
75
Stage (ft)
70
65
60
55
B
10000
9000
Q75 Max
8000 Median Mini
Q25
7000
Discharge (cfs)
6000
5000
4000
3000
2000
1000
0
Figure 3-38. Box and whisker diagrams showing the monthly variations in stage (A)
and discharge (B) at the Jennings gage on the Alapaha River.
3-56
8055
Q75 Max
7055 Median Mini
Q25
6055
Discharge (cfs)
5055
4055
3055
2055
1055
55
Figure 3-39. Box and whisker diagram showing the monthly variations in
discharge at the Jasper gage on the Alapaha River.
1255
Q75 Max
1055 Median Mini
Q25
855
Discharge (cfs)
655
455
255
55
Figure 3-40. Box and whisker diagram showing the monthly variations in
simulated discharge at the Alapaha Rise.
3-57
TAB 4
4.0 ECOLOGICAL ANALYSES
Hydrologic conditions include the principal physical forces which influence stream ecosystems
(Poff et al., 1997; Poff and Ward, 1989). Flow influences ecological integrity directly (Poff and
Alan, 1995), or indirectly via other factors such as water quality, physical habitat availability, fish
passage, etc. (Schlosser, 1991; Poff et al., 1997). The hydrologic description provided in
Section 3.0 serves as the framework which structures the ecological communities of the river,
including those in the river channel and adjacent floodplains.
This section characterizes the ecology of the Alapaha River. As stated in previous sections, the
Suwannee basin (which includes the Alapaha River) is a significant bio-geographic transition
zone in Florida, with many species of flora and fauna reaching their southernmost limits of
distribution in the U.S. in the Suwannee region. A number of plant species reach the southern
or northern limits of their distribution in the southeastern U.S. in the Suwannee region (Clewell,
1985; Abbott and Judd, 1998) and over half of the native freshwater fishes found in Florida river
systems occur only in or west of the Suwannee (Bass and Cox, 1985; Bass, 1991).
4.1 General Description
4.1.1 Physical Setting
The Alapaha can be characterized as a southeastern coastal plain, blackwater stream which
originates in the coastal plain of Georgia, west of the Okeefenokee Swamp. The total length of
the river is 130 miles, of which 22.6 miles are located in Florida. The majority of the Alapaha
River Basin, which comprises 1840 square miles, is located in Georgia (see Figure 2-1).
As noted in Sections 2 and 3, the Alapaha flows into the Suwannee River in northern Florida
under high flow and flood conditions. Above State Road (SR) 150, the river is incised into a
rock bound channel with rock shoals. Below SR 150, the river floodplains broaden for a short
distance and sinkholes begin to capture a significant portion of the river (Figures 2-28 through 2-
31). As previously described in Section 3.0, the Florida portion of the river flows over karstic
limestone, and under low to moderate flow conditions, river flow is captured by a series of
sinkholes within the streambed. The Alapaha River is also known as the River of Sand for this
reason. The water travels underground via caverns and conduits, then discharges from springs
along the Suwannee River, most notably the Alapaha Rise and Holton Creek Rise (Figures 2-25
and 2-36, respectively; Figure 4-1). These are first and third magnitude springs, respectively
(Ceryak et al., 1983).
The Alapaha River lies in the Tifton Upland/Tallahassee Hills sub-ecoregion of the Southern
Plains eco-region (Griffith, et al., 1994). Using Becks (1965) classification, the lower portion of
the Alapaha River is a calcareous stream reflecting the influence of springs and karst
topography. The area is characterized by low to moderate relief with soils ranging from well
draining sands to clay. Karst influences on topography and physiography are evident, in the
form of sinks and depressional features.
4-1
Figure 4-1. Locator map of the Alapaha River in Florida showing major roadways, Alapaha and
Holton Creek rises, and the river mile system.
4-2
4.1.2 Riparian Area
The riparian wetland vegetation has been characterized and classified by the SRWMD 1994-
1995 Land Use and Cover Project and from the National Wetlands Inventory (NWI). The land
use and cover data were photo-interpreted from 1994-1995 National Aerial Photography
Program (NAPP) 1:40,000 color infrared photography. Photo interpretation was done using
United States Geological Survey 7.5 quadrangle base maps (SRWMD, 1998). Data were
classified based on a modified Florida Land Use Cover and Forms Classification System
(FLUCFCS), originally established by the Florida Department of Transportation. Similar cover
types were grouped into polygons using mylar overlay and then digitized into ARC/INFO.
Ground truthing was performed and overall accuracy was determined to be 85% (SRWMD,
1998).
The National Wetlands Inventory (NWI) (USFWS, 2002) is a program established under the
United States Fish and Wildlife Service with the purpose of characterizing the extent and status
of the Nations wetland, deepwater, and other wildlife habitats. NWI maps contain information
on location and type (classification) of wetlands and deep-water habitats (stream, lakes, and
estuaries). NWI information is based on the interpretation of high-altitude aerial photographs,
with a minimum required mapping resolution of 2 acres. Additionally, it should be noted that the
mapped area is the approximate location and size of the wetland, relative to geographic
features (e.g., roads) and annual and seasonal variation (e.g. in dry years wetland extent will be
limited compared to wetter years; same for dry vs. wet seasons within a year) at the time the
aerial photos were taken. Accuracy is limited to 30-50 feet (USFWS, 2002).
National Wetland Inventory data show most of the riverine habitat as palustrine forested, with
limited patches of palustrine emergent vegetation (Figure 4-2). Land use data show adjacent
forests as being primarily temperate hardwoods, with few areas of managed pine plantation and
oak-pine-hickory forests (Figure 4-3). Based on the 10 year floodplain, a sizable forested
floodplain exists adjacent to the Alapaha River which is generally categorized as seasonally
flooded, with northern most portions being described as temporarily flooded (Figure 4-4).
However, due to the steep gradient and incised channels in the river, riparian vegetation
adjacent to the river is generally temperate hardwoods and improved pasture (SRWMD 1995
land use coverage), neither of which is related to floodplain inundation. On the Alapaha,
regularly inundated wetlands or swamps, such as those that typically form headwaters or those
wetlands adjacent to less incised rivers, are lacking. National Wetland Inventory data show little
seasonal flooding adjacent to the river, with a slight increase in the width of this flooding
downstream of river mile 15. Nonetheless, even in a incised river, the forested floodplains play
an important role in both direct and lateral leaf litter fall into the river.
Leaf litter provides an important source of energy (i.e., carbon), particularly in lotic aquatic
ecosystems. There are two ways in which leaf litter reaches the channel. The first is the result
of the direct descent of leaf material into the channel, which clearly occurs irrespective of flow
conditions. The second manner in which leaf litter may enter the channel occurs during high
flows. During these periods, organic materials that have accumulated on the floodplain floor
can be mobilized and translocated into the river channel. Upon reaching the channel, further
downstream deposition of leaf litter occurs as a function of flow.
Parts of the Alapaha River located in Georgia would be considered blackwater streams,
reflecting the dark color of the water as a result of leached tannic compounds derived from the
decomposed leaf litter.
4-3
Figure 4-2. Map showing the National Wetlands Inventory habitat categories within the 10 year
floodplain on the Alapaha River in Florida.
4-4
Figure 4-3. Map showing relevant vegetation categories as provided by the Suwannee River
Water Management Districts land use coverage within the 10 year floodplain on the Alapaha
River of Florida.
4-5
Figure 4-4. Map showing the National Wetlands Inventory water regime categories within the
10 year floodplain on the Alapaha River of Florida.
4-6
4.2 Water Quality
Water quality in the Alapaha is an issue in terms of both the impact of surfacewater entering the
groundwater system, and the impact of surfacewater quality on aquatic habitat and associated
Figure 4-5. Locator map of the Alapaha River, showing the main water
quality and biology station (ALA010), and a supplementary biology station
(ALA020), maintained by the Suwannee River Water Management District.
fauna. Available water quality data were discussed in a previous report prepared for the
SRWMD (Water Research Associates, 2005). Long term water quality data were limited to one
station from the SRWMDs water quality monitoring program, located on the river near Jennings
(ALA010) (Figure 4-5). Parameters sampled for the long term station (ALA010) include the
following: alkalinity, chlorophyll, color, conductivity, dissolved oxygen (DO), nitrate+nitrite
species (NOx), orthophosphate, pH, temperature, total Kjeldahl nitrogen (TKN), total nitrogen
(TN), total organic solids (TOS), total phosphorous (TP), total suspended solids (TSS), and
turbidity.
Mean annual dissolved oxygen (DO) ranged from above 7 to 8.5 mg/L in the Alapaha River
above the sinkholes, indicating there are no DO problems (Figure 4-6). Plots for additional
parameters are located in Appendix 4-A. A time series of DO as a function of flow showed the
full range of DO values occurred at low flows (Figure 4-7). All DO values were above 5 mg/l,
except on two occasions with vastly different flow conditions (i.e., 270 cfs and 6292 cfs) (Figure
4-7).
4-7
Figure 4-6. Mean annual dissolved oxygen (mg/l), with 95% confidence limits, for the Alapaha
River in the Suwannee River Water Management District. (Source: Janicki Environmental, Inc.,
2004).
4-8
Figure 4-7. The relationship between dissolved oxygen at Suwannee River Water Management
District station ALA010C1 and flow between 1989-2003.
4.3 Benthos
Benthic biological data were previously summarized (Water Research Associates, 2005) and
reviewed (Janicki Environmental, Inc., 2004). The SRWMD, as part of their water quality
monitoring program, have collected benthic invertebrate data at one long term station located on
the river near Jennings (ALA010). A second station (ALA020) provides data for an abbreviated
period of record (1990-1991), consisting of only 7 samples (Figure 4-5). The macroinvertebrate
data are qualitative, as they were collected with a D-frame dip net and targeted selected micro-
habitats (e.g., leaf packs, root mats, submerged and emergent aquatic vegetation, woody snag
habitat, etc.). While this approach focuses on identifying the full diversity of the system, lack of
quantitative data limits certain analyses.
Mean annual species richness in the Alapaha River ranged from approximately 22-45 species
(Figure 4-8), while the mean annual number of Genera ranged from 19-37 (Figure 4-9). Mean
annual Shannon-Weaver Diversity ranged from 3.5 - 4.75 (Figure 4-10), while Pielous Eveness
ranged from 1.0 to just under 1.4 (Figure 4-11).
4-9
Figure 4-8. Mean annual benthic invertebrate species richness, with 95% confidence limits, for
the Alapaha River in the Suwannee River Water Management District. (Source: Janicki
Environmental, Inc., 2004).
4-10
Figure 4-9. Mean annual number of benthic invertebrate genera, with 95% confidence limits,
for the Alapaha River in the Suwannee River Water Management District. (Source: Janicki
Figure 4-10. Mean annual benthic invertebrate diversity (expressed using the Shannon-Weaver
Diversity Index), with 95% confidence limits, for the Alapaha River in the Suwannee River Water
Management District. (Source: Janicki Environmental, Inc., 2004).
4-11
Figure 4-11. Mean annual measure of eveness (using Pielous Eveness Index), with 95%
confidence limits, for the Alapaha River in the Suwannee River Water Management District.
(Source: Janicki Environmental, Inc., 2004).
The total number of species reported for station ALA010 was over 300, while at station ALA020,
which had significantly fewer samples, was 100 (Figure 4-12). Species richness was
categorized by taxonomic group, and Chironomidae dominate at station ALA010, followed by
Ephemeroptera and Coleoptera (Figure 4-12). The number of species belonging to
Chironomidae was approximately equal to the number in Coleoptera at station ALA020 (Figure
4-12). Trichoptera and Plecoptera are present at station ALA010, but are absent at station
ALA020 (Figure 4-12). Relative abundance was also categorized by taxonomic group at the two
stations (Figure 4-13).
The fauna at station ALA010 was numerically dominated by species that are characteristic of
flowing waters and that are not typically collected from slower flowing streams (Pescador et al.,
1995; Smith et al., 1998; Goldschmidt, 2006; Soil & Water Conservation Society of Metro
Halifax, 2006):
Chironomidae larvae: Polypedilum illinoense and Rheotanytarsus exiguus group
Trichoptera larvae: Hydropsyche rossi and Chimarra sp.;
Simulium sp. (Simuliidae); and
Torrenticola sp. (Acari, Torrenticolidae).
The additional station (ALA020) was only surveyed during 1990-1991. However, many of the
common, lotic species at station ALA010 were not collected at ALA020. The most commonly
collected species at ALA020 included gastropods (Campeloma sp. and Viviparus georgianus),
the riverine and marsh-dwelling caridean shrimp Palaemonetes paludosus (Carroll, 1996),
whirligig beetle Dineutus discolor and the littoral haliplid beetle Peltodytes sexmaculatus.
4-12
Figure 4-12. Stacked bar chart showing invertebrate species richness as distributed
throughout the major taxonomic groups in the Alapaha River. (Source: Janicki
Figure 4-13. Stacked bar chart showing invertebrate percent abundance, by major taxonomic
group, in the Alapaha River. (Source: Janicki Environmental, Inc., 2004).
4-13
4.4 Mussels
Based on the available literature, only one species of unionid mussel has been reported from
the Alapaha River in either Florida or Georgia: Quadrula kleiniana (Suwannee Pigtoe).
Quadrula kleiniana has been collected from the Alapaha River in both south Georgia and north
Florida as well as in the Withlacoochee, Santa Fe, New, and Suwannee rivers (Williams 2004).
There are at least 10 records of its occurrence in the Alapaha River, primarily near Statenville,
Georgia and Jennings, Florida (Williams 2004). The waterways in which this species has been
collected are described as medium to large creeks and rivers, with muddy sand to mixed sand
and gravel substrate, in slow to moderate current (Williams 2004).
Williams (2004) reports that the conservation status of Quadrula kleiniana needs to be
reevaluated since, until recently, this species had been considered to be the same species as
Quincuncina (=Quadrula) infucata. However, Williams (2004) speculated that this species is in
a decline in the Suwannee River drainage basin.
The main objective of Williams (2004) study was to ascertain the status of Medionidus walkeri
(Suwannee Moccasinshell) in this drainage. He speculated that, because there is relatively little
gravel/rocky substrate in the Alapaha River, it was unlikely that viable populations of Medionidus
walkeri were ever established. Neither of these species is listed as either endangered or
threatened (U.S. Fish and Wildlife Service, 1998; Florida Fish & Wildlife Commission, 2004).
Quadrula kleiniana is found to co-occur with Medionidus walkeri and Pleurobema pyriforme in lotic
waters ranging in size from mediumcreeks to rivers. It occurs in sediments that are
characterized as muddy sands, and mixed sand and gravel. Current velocities range from slow
to moderate (Williams and Butler, 1994). The host of the glochidia is unknown. The related
species Quadrula cylindica parasitizes Cyprinella spiloptera (spotfin shiner), Cyprinella galactura
(whitetail shiner), and Notropis amblops (bigeye chub) (Louisiana Department of Wildlife and
Fisheries Natural Heritage Program 2006). Another related species, Quadrula asperata,
parasitizes Ictalurus punctatus (channel catfish) (Haig and Warren, 2003).
Another species of mussel, Medionidus penicillatus (Gulf Moccasinshell), has been historically
reported throughout Alabama, Georgia and Florida in the Apalachicola-Chattahoochee-Flint
(ACF) basin and the Econfina River (USFWS, 1998; USFWS, 2003). It is generally accepted
that sub-populations have been in decline, and extirpated in certain areas, so current
distribution may not be as extensive as the historical records indicate. Medionidus penicillatus
is listed as endangered in the Georgia and State Protected in Alabama. However, the species
has been reported to be present in Florida in the Withlacoochee and New Rivers (Jim Williams,
USGS, Feb. 2006, pers. comm.). Additionally, the main host species for the glochidia in the
ACF basin were reported to be Etheostoma edwini (Brown darter) and Percina nigrofasciata
(Black banded darter). Both species of darters have been reported in rivers within the
Suwannee basin (Hellier, 1967; Bass in Livingston, 1991).
4-14
Figure 4-14. Historical and current distribution of Quincuncina (=Quadrula) kleiniana within the
Suwannee River drainage, Florida. = historical site only; = both historical and recent sites;
= recent site only. (Source: Blalock-Herod and Williams, 2004).
Figure 4-15. Quadrula kleiniana, Suwannee Pigtoe (Source: Williams, 2004).
4-15
4.5 Fish
As with mussels, little is known about the speciation and ecological relationships of fish in the
Alapaha. The following discussions draw on information about fish in other rivers of the
Suwannee system.
Current fish distributions are related to several factors, such as, dispersal from source (e.g.,
Mississippi/West Indian) and major sea level cycles. Peninsular Florida is known as an
important region for biological endemism (Gilbert, 1987). The physical separation of the
peninsula from the panhandle portion of Florida, as well as other southeastern states, likely
occurred as a result of fluctuating sea level and the formation of a salt-water barrier in the
northern part of the peninsula (Gilbert, 1987). This is evidenced by relict shorelines, such as the
Cody Escarpment. The Cody Scarp serves as an important zoogeographic boundary between
the Northern Highlands and the Coastal Lowlands (Gilbert, 1987). All rivers that cross the
scarp other than the Suwannee, drain underground through swallets and reappear as
resurgences further downstream.
The majority of available information on fish distribution within the Suwannee Basin was for the
Suwannee and Santa Fe Rivers and derived from Hellier (1967), Bass (1991), Swift et al.
(1986), and the University of Florida Museum of Natural History Icthyology Collection, which
contained mostly entries for the lower, tidally influenced portion of the Suwannee River
(accessed online Feb.-Mar, 2005). Species lists complied from Hellier (1967) and Bass (1991)
are located in Appendix 4-B. The records obtained from the UF museum collection were
determined to not be applicable to the Alapaha River. Most zoogeographic accounts and
distribution studies were completed on a larger scale than the Alapaha Basin and do not provide
enough resolution to differentiate between the Suwannee and its other tributary streams.
Information was solicited from the Georgia Department of Natural Resources (GDNR), who was
able to provide the only site-specific information available for the Alapaha River (Mike Geihsler,
GDNR, Mar. & June, 2005, pers. comm.).
4-16
Table 4-1. List of fish species recorded in the Georgia portion of the Alapaha River. Data
obtained from the Georgia Department of Natural Resources standardized sunfish sampling.
Species listed in alphabetical order by scientific name. Sampling was conducted in 1998 and
2000.
Scientific Name Common Name

Ameiurus nebulosus Brown bullhead
Centrarchus macropterus Flier
Enneacanthus gloriosus Bluespotted sunfish
Esox americanus Redfin pickerel
Esox niger Chain pickerel
Ictalurus punctatus Channel catfish
Lepomis auritus Red breast sunfish
Lepomis gulosus Warmouth
Lepomis macrochirus Bluegill
Lepomis marginatus Dollar sunfish
Lepomis megalotis Longear sunfish
Lepomis microlophus Redear sunfish
Lepomis punctatus Spotted sunfish
Micropterus notius Suwannee bass
Micropterus salmoides Largemouth bass
Pomoxis nigromaculatus Black crappie
Data on fish communities in the Alapaha River were limited to standardized sunfish sampling
conducted in the Georgia portion of the river, as provided by the Georgia Department of Natural
Resources (GDNR). The most abundant sunfish species was by far the Lepomis auritus
(Redbreast sunfish). Additional abundant species, in alphabetical order, include Lepomis
macrochirus (Bluegill), Esox niger (Chain pickerel), Lepomis marginatus (Dollar sunfish),
Micropterus salmoides (Largemouth bass), Lepomis punctatus (Spotted sunfish), and Lepomis
gulosus (Warmouth) (Figure 4-16). A complete species list from the GDNR sunfish sampling
in the Alapaha is shown in Table 4-1.
4-17
Figure 4-16. Drawings of several members of the sunfish family: Lepomis aurtus (Redbreast
sunfish), Lempomis macrochirus (Bluegill), Lepomis gulosus (Warmouth) and Lepomis
punctatus (Spotted sunfish). (Source: http://floridafisheries.com/images/raverart/)
4.5.1 Groups of Fish Present in the Suwannee Drainage
Family Cyprinidae
Cyprinids represent the largest family of fish in North America and most notably include the
minnows (Figure 4-17). In addition to minnows, shiners, dace and chubs belong to this family.
The largest genus of Cyprinids is Notropis, which are typically small, mid-water fishes that
consume small crustaceans and insects.
In general, Cyprinids can occupy a variety of habitats ranging from headwater bogs, swamps,
springs, rivers, ponds and lakes. Often times, many different species of minnows can occupy a
single stretch of a moderately sized stream. Because of their small size, a large number of
minnows can occupy a relatively small space and still find adequate food and shelter.
4-18
Figure 4-17. Photographs of two species of Cyprinids, Notemingonus crysoleucas (Golden
shiner) and Notropis hypselopterus (Sailfin shiner).
(Source: http://www.samford.edu/schools/artsci/biology/zoology/vertzoo-05s/photos/).
Family Fundulidae
Fundulids include killifish and topminnows (Figure 4-18). These fish are generally small and
swim mainly at the top of the water column, near the surface (hence the name topminnow).
Like Cyprinids, Fundulids can occupy a range of habitats including streams, rivers, lakes,
ponds, and marshes. Terrestrial insects and insect larvae make up a large portion of the diet for
a number of species belonging to this family, along with crustaceans and small water plants.
4-19
Figure 4-18. Photographs of two representative species of Fundulids, Fundulus seminolis
(Seminole killifish) and Fundulus lineolatus (line top minnow).
(Sources: http://www.nanfa.org/NANFAregions/fl_cent/fl2003/FRsemikilli.jpg
http://www.cnr.vt.edu/efish/families/images/gifs/linetopm.gif)
Family Percidae
Darters are the second most diverse family of fish, after Cyprinidae. The genus Percina and
Etheostoma represent darters in the Suwannee drainage. They typically inhabit fast flowing
streams, or riffle areas where depth is shallow and velocity increases. Through a combination
of behavior and morphology, darters avoid being carried downstream with the current. Darters
are a benthic group of fishes that completely lack, or have greatly reduced, swim bladders (gas
bladders). These fish are also typically strong swimmers which can dart about from one point
of cover to the next. They spend most of their time darting about on the bottom of streams and
lakes eating small crustaceans and insects. Percina includes the most primitive darters, and
they have retained a small swim bladder and generally swim above the stream bottom more so
than other darters. The genus Etheostoma is the largest genus of North American fishes. In the
Alapaha, the brown darter (Percina) and the blackbanded darter (Etheostoma) has been
identified as part of this report as probable inhabitants that would be associated with certain
flow/velocity preferences (Figure 4-19). These habitat preferences are used in the development
of the Ecosystem Functions Model, one of the techniques used in the ecological determination
of a low flow MFL on the Alapaha River (Section 5.1.2.1).
Being able to occupy a riffle habitat has certain advantages for darters, including affording some
protection against terrestrial predators, as well as having access to an often under-exploited
food supply. Riffles provide a degree of camouflage from the surface, making the fish less
visible to predators. Additionally, insects often lay eggs near rocks or logs which are often
associated with riffles. Darters are able to inhabit and feed on these eggs, whereas other fish
may not be able to maintain position in the riffle long enough to feed.
4-20
Figure 4-19. Photographs of two darter species in the Suwannee drainage, Etheostoma edwini
(brown darter) and Percina nigrofasciata (blackbanded darter). (Source:
http://www.samford.edu/schools/artsci/biology/zoology/).
Family Centrarchidae
Centrarchids, which include sunfish and basses, generally prefer slow moving or sluggish
waters and are common inhabitants of lakes and reservoirs. In riverine environments,
centrarchids can often be found near pools or areas with aquatic vegetation, stumps, logs, etc.
Changes in water level can affect spawning, specifically rapid drops in water level can cause
spawning failure. Habitat suitability curves were initially developed for a number of sunfish
species to address concerns over river impoundments and the possible rapid change in water
level associated with the establishment of dams and water releases from the dams. However,
because these species prefer slow moving waters, they are not considered to be the best taxa
for use in the development of MFLs.
One exception is the Suwannee Bass (Micropetus notius), which is listed by the State of Florida
as a Species of Special Concern (Bass et al., 2004). The main prey item of the Suwannee Bass
is the crayfish Procambrus spiculifer (Figure 4-20), which has specific velocity requirements
(Figure 4-20). The Suwannee bass is confined to flowing water environments and is native to
the Suwannee and Ochlockonee River drainages (Gilbert, 1978; Hurst et al., 1975, Stevenson,
1976). The species has historically been uncommon on the Ochlockonee system, while the
largest populations are reported in the Santa Fe River (Bass, 1974; Bass and Hitt, 1973). The
Suwannee bass was also introduced, presumably by anglers, to the St. Marks River System
where it appears they have successfully colonized the area and are abundant. The species was
collected from the Suwannee, Santa Fe, St. Marks, and Ochlockonee River systems by the
Florida Imperiled Fish Species Investigation (Bass et al., 2004). The summation provided by
the Imperiled Fish Species Investigation stated that, although the Suwannee bass do not appear
4-21
to be presently threatened, they should remain a Species of Special Concern on the Florida
Fish and Wildlife Conservation Commission Register. Water quality conditions in the Santa Fe
and Suwannee Rivers was cited as a cause for continued monitoring of the Suwannee bass
population stability in the area (Bass et al., 2004).
Figure 4-20. Drawing of Micropterus notius (Suwannee Bass) and its prey species, the crayfish
Procambrus spiculifer. (Source: http://en.wikipedia.org/wiki/Image:Micropterus_notius.jpg;
www.crayfishworld.com/image/02Pspiculifer2.jpg)
Family Ictaluridae
The catfish family is the largest family of fresh-water fish endemic to North America. Catfishes
are generally warmwater fish that are more tolerant of low dissolved oxygen conditions than
most other groups of fish. They have sensory barbels which enable them to feed on insects,
crustaceans and other fish at night or during the day in turbid waters. Because of their
tolerance for low oxygen and low light conditions, catfish are generally bottomfeeders. While
bullhead catfish and other largers species of catfish are commonly caught by anglers, other
members of the family, smaller in size, are seldom observed (i.e., madtoms). Channel catfish
are very common and the species most typically farm raised. They prefer cooler, deeper,
cleaner water than bullhead catfish (Figure 4-21).
4-22
4.6 Summary
The ecological information available for the Alapaha River has been summarized in the
preceding paragraphs. Information on major vegetative communities is available from the
SRWMDs land-use and cover data, and from information collected by the NWI. Because the
Alapaha is a fairly incised river, relative to other rivers in Florida, it does not have the extensive
riparian and wetland vegetation typically found.
Water quality data available through the SRWMDs monitoring program included an extensive
list of parameters. Benthic biological data were also available from the SRWMDs monitoring
program. As with the water quality data, benthic data were collected at the long-term water
quality station and seven samples were collected during 1990-1991 at a second station located
just above the confluence with the Suwannee River.
The occurrence of unionid mussels has been reported in the Alapaha, but published information
was largely only available for mussels in the Suwannee and Santa Fe Rivers. Numerous fish
species are likely to occur in the Alapaha River. However, specific sampling efforts in the
Alapaha River are lacking. Information on fish distribution gathered from studies of other rivers
within the Suwannee River drainage and from sampling efforts conducted by the Georgia
Department of Natural Resources in the Georgia portion of the Alapaha River is useful.
4-23
TAB 5
5.0 ECOLOGICAL BASIS FOR A MINIMUM FLOW FOR THE ALAPAHA RIVER
A minimum flow that protects essential habitats of the Alapaha River from significant
environmental risk should be based upon the following criteria:
The maintenance and protection of essential fish foraging habitat, including snag habitat;
The maintenance and protection of suitable habitat for fresh-water mussels (e.g.,
Quadrula kleiniana, Suwannee Pigtoe) and host species for their parasitic
developmental stages;
The preservation of the frequency and duration of hydrologic connectivity between upper
and lower reaches of the Alapaha River, ensuring both adequate minimum depths for
fish passage and the maintenance of historic connectivity with the Suwannee River.
The available physical habitat for biological organisms in streams generally consists of the
interaction of stream depth and velocity (Bovee et al., 1998); each of which is related to flow.
Substrate and cover characteristics are additional parameters that affect habitat suitability,
although depth and velocity are the primary determinants (Bovee et al., 1998). The focus on
physical habitat characteristics is based on the lack of a direct relationship between water
quality proxies (e.g., dissolved oxygen) and stream flow (Figure 4-7, Appendix 4-A). While
water quality is an important water resource value, in this portion of the Alapaha River, there is
no significant relationship between dissolved oxygen and flows.
5.1 Methods
The establishment of MFLs for the Alapaha River relies on the weight-of-evidence approach
based on using the following three methods:
Wetted Perimeter analysis,

Ecosystem Functions Model (EFM), and
Fish Passage analysis.
5.1.1 Wetted Perimeter
The wetted perimeter of a stream transect is defined as the width of the streambed and stream
banks in contact with water for an individual cross section (Parker and Armstrong, 2002).
Wetted perimeter is used as an estimate of the amount of habitat available to aquatic organisms
under different flow conditions. Generally, greater extents of wetted perimeter in a stream or
river are associated with increased habitat availability for fish and macroinvertebrates. Changes
in wetted perimeter represent how alterations in stream flow affect the morphometry of the
stream (Parker and Armstrong, 2002). For example, given two reaches of a stream of equal
depth but different channel widths, the wetted perimeter in the reach with the narrower channel
will be more responsive to changes in flow than the reach with the wider channel. Basically, a
narrow stream will go out of bank faster than a stream of greater width (Parker and Armstrong,
2002; Water and Rivers Commission, 2003).
In theory, as the flow regime changes there should be a stream flow at which wetted perimeter
increases dramatically (i.e., an inflection point) (Parker and Armstrong, 2002; Water and Rivers
Commission, 2003; cf. Figure 5-1). This inflection point or threshold demarcates a potential
minimum flow (Gippel and Stewardson, 1998; Parker and Armstrong, 2002). In practice, such
inflection points are not always clearly defined or there can be multiple inflection points (Parker
5-1
and Armstrong, 2002). The identification of the specific flow can be subjective, although there
are more rigorous mathematical solutions to identify the inflection point (Gippel and Stewardson,
1998). Expert knowledge of the system is often used to identify the most meaningful inflection
point.
500.0
499.5
499.0
498.5
Elevation (ft)
498.0
Bank Stations
497.5
497.0
496.5
496.0
0 5 10 15 20 25 30
Station (ft)
20.0
15.0
Wetted Perimeter(ft)
Point of Maximum
10.0 Curvature
5.0
0.0
0 5 10 15 20
Discharge (cfs)
Figure 5-1. Examples of a stream cross-section (top) and the relationship between stream
flow and wetted perimeter (Adapted from: Parker and Armstrong, 2002).
The wetted perimeter technique has been used, in conjunction with other methods, to establish
MFLs in rivers of the Southwest Florida Water Management District (SWFWMD) including the
Alafia (SWFWMD, 2004), Myakka (Kelly et al., 2005) and Peace Rivers (SWFWMD, 2002).
Wetted perimeter has also been used to evaluate fisheries habitat in the western United States
(Swift, 1976; Moratz and Staley, 1986; Leath, 1989) and has been applied in concert with other
methods to estimate available habitat in Australian rivers (Tunbridge, 1988; Tunbridge &
Glenane, 1988; Anderson & Morison, 1989).
The upper reach of the Alapaha River was selected for both wetted perimeter analysis and use
of the Ecosystem Functions Model (see following section). The upper reach (above river mile
18, which is the approximate location of the swallets reach of the river) experiences more
variable velocities than the lower reach (Figures 5-2 and 5-3). For the establishment of an MFL,
wetted perimeters were calculated for the 11 transects in the upper reach of the river (Figure 5-
4). Wetted perimeter was derived from HEC-RAS, which calculates wetted perimeter as the
linear distance along the transect that comes into contact with the water. Wetted perimeter
5-2
Figure 5-2. Location of HEC-RAS transects in the Alapaha River in Florida.
5-3
> 75% < 75%
Figure 5-3. Bivariate plot of HEC-RAS modeled velocities vs. river mile in the Alapaha
River. The reference line located at river mile 18 shows more variable and higher
velocities above this point on the river and lower velocities below. Note that the range of
velocities is truncated at 1.5 ft/sec, which represents the 70th percentile estimated velocity
in transects above river mile 18. The maximum estimated velocity in the upper reach of
the Alapaha River is 5.20 ft/sec.
5-4
Figure 5-4. Map of HEC-RAS transects in the Alapaha River in Florida selected for wetted
perimeter estimates.
5-5
follows the contour of the HEC-RAS definition of the transect bathymetry from the left most point
along the bank that is wet , across the river bed, to the right most point along the opposite
bank that is wet. The application of this technique requires the assumption that wetted
perimeter is a valid measure of available habitat for fish and macroinvertebrates (Annear and
Conder, 1984; Arthington and Zalucki, 1998).
5.1.2 Instream Flow Methods
Bovee et al. (1998) describe an incremental, multi-faceted process for evaluating the instream
flow requirements of lotic organisms, particularly fishes. This approach, titled Instream Flow
Incremental Methodology (IFIM), considers hydraulic conditions, water quality, temperature
regime, morphology and morphometry of the channel, as well as the physical microhabitat
requirements of the biota in terms of depth, velocity, substrate and cover (Bovee et al. 1998).
The microhabitat requirements for the biota are considered in the Physical Habitat Simulation
(PHABSIM) module of IFIM (Bovee et al. 1998).
PHABSIM was the method initially adopted to provide the habitat-based component of the
approach adopted for establishing MFLs in the District. However, the incised banks and high
stream velocities in the Alapaha River made it impractical and a safety concern to implement.
Alternatively, the Ecosystem Functions Model described below was selected and applied in
place of PHABSIM.
5.1.2.1 Ecosystems Functions Model
The Ecosystem Functions Model (EFM) was selected as a viable alternative to PHABSIM. This
model estimates how the river would respond when presented a given flow scenario and the
system was or was not modified. This method was developed by the California Department of
Water Resources, the U.S. Army Corps of Engineers Hydrologic Engineering Center HEC
(State of California Reclamation Board and US Army Corps of Engineers 2002; Hickey and
Dunn 2004), and Jones and Stokes (1999 and 2000). EFM was originally conceived of as a tool
to address flood control issues in the Sacramento and San Joaquin River Basins in California.
Flood damage under high flows could be evaluated, and the effects of structural modifications
(e.g., levee construction) and restoration of affected riverine and riparian ecosystems could be
modeled. EFM has recently been applied elsewhere within the Suwannee River Water
Management District, on the Upper Santa Fe River, as well as on the Sustainable Rivers
Project, a collaboration of the U.S. Army Corps of Engineers and The Nature Conservancy on
the Savannah River system (WRA, 2006; Hickey and Warner, 2005).
EFM requires the following types of data to estimate ecological responses to flow alterations:
a record of historical flows,

establishment of HEC-RAS transects (see Section 3),
development of a calibrated HEC-RAS model, and
water depth and velocity requirements of key biota for that river system
The EFM approach differs from PHABSIM in that:
data from the many HEC-RAS transects are employed to represent the entire river reach
rather than relying on data collected from just a few albeit specific mesohabitats;
5-6
the historical flow regime is incorporated into the EFM, this includes historical high flows
and low flows whereas the PHABSIM approach is only calibrated for the flows collected
during the field surveys, likely missing significant high and low flows;
HEC-RAS is the hydraulic model employed in the EFM, which is superior to the hydraulic
component of PHABSIM, widely accepted and well documented;
HEC-RAS can be calibrated to fully dynamic simulations capturing the full range of flows
allowing sufficient comparisons between simulated and observed data; long term
comparisons allow added confidence in the models ability in reproducing hydraulic
response;
The HEC-RAS hydraulic component simulates the entire stream reach allowing the EFM
to represent the pool and riffle habitat pervasively found in the Alapaha River.
There are several required steps in the Ecosystem Functions Model:
1) Ecological Analysis: The ecological analysis identifies relationships between river

hydrologic and hydraulic conditions and the rivers ecosystem and geomorphic system.
These relationships reflect requirements of different biota or habitat types in terms of
flow conditions, based on frequency, season, and duration.
Ecological attributes of the river that can be modeled for their inter-relationships with the
hydrologic and hydraulic characteristics include:
estimates of spawning habitat area for fish;

suitability of habitat (defined by depth and current velocity) for aquatic
macroinvertebrate production.
Ecological relationships relevant to setting a MFL in the Alapaha River were identified
after an extensive review of the available literature. Species or taxonomic groups that
were considered to be sensitive to alterations in stream velocity and depth were of
particular interest. The preferred depth and velocity ranges for the identified taxa are
listed in Table 5-1. These taxa included:
Aquatic insect larvae - Habitat Suitability Indices for three taxonomic groups
(Ephemeroptera, Trichoptera, and Plecoptera) known to occur in the Alapaha
River were developed by Gore et al. (2001).
Crayfish - Procambarus spiculifer has been identified as the primary prey for the
Suwannee Bass (Micropterus notius) and as a secondary prey for Largemouth
Bass (Micropterus salmoides) (Schramm and Maceina, 1986). Both fish species
are recreationally important in the river, and the Suwannee Bass is a state listed
Species of Special Concern.
Darters Many species of Percidae have a preference for riffle habitats (Lee et
al. 1980; Etnier et al. 1993. Marcinek et al 2003). These include two species
known to occur in the Suwannee River drainage and known to occur in the
Georgia portion of the Alapaha River: the brown darter (Etheostoma edwini) and
the blackbanded darter (Percina nigrofasciata).
Additionally darters are host species for the parasitic lifestage of certain unionid
mussels (Bigham 2002). By establishing a flow regime protective of darters it is
possible that protection is provided for habitat that can be colonized by unionids
(Gore et al., 2001).
5-7
2) Statistical Hydrology Analysis: This analysis translates the depth and velocity
relationships developed in the Ecological Analysis into discharges with specified
frequencies, seasons, and durations. The statistical analysis uses existing flow records
as the basis for determining the flows that satisfy the habitat-defined requirements
developed in the Ecological Analysis.
Alapaha River flows ranging from 40 to 180 cfs, in 10 cfs increments, were considered
for the EFM. These flows represent the range within which the depth and velocity
preferences of the key taxa in Table 5-1 are most likely to occur, as modeled in HEC-
RAS. These flows also represent the historical range of flows up to the 75 percent
exceedance flow, based upon the flow-duration curve at the USGS gage at Jennings, FL
(Figure 5-5). Also, due to the significant effect of the Suwannee River on stage (and,
thus, depth) in the Alapaha River, the HEC-RAS model was run for two different
Suwannee River stage scenarios, the 80 percent exceedance stage and the 60 percent
exceedance stage. These two stage scenarios correlate highly with the occurrence of
the range of Alapaha River flows used in the statistical hydrology analysis. At transects
above river mile 18, there was no difference in the modeled velocities and depths from
HEC-RAS output between the two stage scenarios, suggesting that backwater
conditions in the Alapaha River created by Suwannee River stages do not extend into
the reach chosen for application of the EFM.
None of the target taxa (Table 5-1) for the EFM has seasonally-specific requirement for
the velocities or depths. Therefore, the analysis was not seasonally specific, and there
was no seasonal adjustment for the determination of critical low flows.
An annual frequency for each low flow event was used for the application of EFM to the
Alapaha River. The annual frequency for low flow events was dictated by the relatively
short life-spans for species in the selected taxonomic groups, especially the
macroinvertebrates. The selection of an annual frequency for low flow events ensures
viable populations over the short-run as well as the survival of every year-class.
3) Hydraulic Analysis: This analysis determines the hydraulic responses of discharges

estimated in the previous step (i.e., Statistical Hydrology Analysis). The statistically
determined discharges form the input to a hydraulic model for the calculation of
corresponding depths and velocities. HEC-RAS, a hydraulic model developed by the
Corps of Engineers (see Section 3.4), is used in its steady-state format to perform the
hydraulic analyses at all transects (Figure 5-2) throughout the system.
Output from the model includes:
water surface elevation,

depth,
velocity, and
wetted perimeter at points along each of the transects.
5-8
10000
Alapaha River near Jenning discharge (cfs)
1000
100
10
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Figure 5-5. Flow-duration curve for the Alapaha River at the USGS Gage at Jennings
(02317620).
4) Ecological Interpretation: A conservative estimate of suitable habitat, as a function of

flow, was determined through an analysis of depth and velocity at intervals along each
transect. Combinations of depth and velocity that satisfy both requirements for each
species are deemed suitable habitats.
Graphs are produced that depict the proportion of suitable habitat (vs. total available
habitat) as a function of flow (40 to 180 cfs range). Graphical summaries were produced
for flows up to the 75 percent exceedance flow at a water depth of 2.0 feet, at each of
four velocities (0.5, 1.0, 1.5, and 2.0 feet sec-1). Stream depths of less than two feet
were not included in this analysis due to inconsistencies in the model output below this
depth criterion. A two feet depth requirement is conservative, yet still below the upper
bound of each taxonomic groups depth preference.
5) Limits of Significant Risk: The MFL will be the flow that corresponds to a 15%
reduction in available habitat at a depth of 2.0 feet. The adoption of a 15% reduction in
habitat is consistent with the peer reviewed approach used by the Southwest Florida and
St. Johns River Water Management Districts to determine the limit of significant risk to
the available habitat (Gore et al. 2002; Southwest Florida Water Management District
2002 and 2004; Lower Suwannee River MFL, WRA 2005). The depth of the water
column chosen to evaluate the MFL (2.0 feet) is protective of the requirements of the
taxa of concern for the Alapaha River (Table 5-1). The range of velocities chosen to
evaluate the MFL (0.5 feet sec-1 2.0 feet sec-1) is protective of at least some portion of
the range of preferred velocities for each of the key taxa chosen for this study (Table 5-
1).
5-9
Table 5-1. Summary of velocity and depth preferences for taxa chosen for the Ecological Analysis
step of the Ecosystem Function Model.
Velocity Depth
Taxa (ft/sec) (feet) Reference
Brown darter (Etheostoma edwini) and Prime: Williams, 1981.
Blackbanded darter (Percina 0.98-2.34 0.33-4.27 Supplemental: Hughey,
nigrofasciata) 2003; Page, 1983.
Schramm and Maceina,
Crayfish (Procambarus spiculifer) 1.47-2.93 1-4
1986
Ephemeroptera 0.33-1.08 1.64-2.33 Gore et al., 2001
Plecoptera 0.33-1.08 1.64-2.62 Gore et al., 2001
Trichoptera 0.33-1.08 1.64-3.12 Gore et al., 2001
Redear Sunfish (Lepomis microlophus) 0.03-0.33 0.33-3.94 Twomey, 1984
5.1.3 Fish Passage
The term fish passage refers to the minimum water depth an organism requires to successfully
navigate a stream channel. Guidelines for fish passage are typically based on body dimension
measurements of several species of adult fish (Hupalo et al., 1994). Few studies have actually
documented minimum water depths required to maintain fish passage, and it is unknown how
many shallow obstructions can be navigated by fish before health and vitality are compromised
(Hupalo et al., 1994). Most studies on fish passage involve adult salmonoid fishes in cold-water
streams. Passage depths of between 0.6 and 0.8 feet were calculated for Chinook salmon and
large trout, respectively (Thompson, 1972, as cited by Hupalo et al., 1994). Minimum water
depths of at least 0.6 feet have been applied previously in Florida (Southwest Florida Water
Management District, 2002, 2005).
Fish passage throughout the Alapaha River was assumed to require water depths of at least 0.6
feet as utilized for other MFL determinations in Florida as successfully peer reviewed
(Southwest Florida Water Management District, 2002, 2005). The longitudinal connectivity that
this minimum depth permits should be maintained throughout the river at a frequency and
duration that is consistent with its historical occurrence. The 0.6 foot criterion for fish passage
was used both for corroboration of the wetted perimeter and EFM-based MFL, as well as for
setting a mid-range MFL. Fish passage during low flow conditions was evaluated for four
different flows which bracket the minimum flows identified in the wetted perimeter and EFM
analyses (100, 110, 120, and 130 cfs) at the five shoal transects that are located above river
mile 18 (Figure 5-4).
The mid-range MFL applies to connectivity in the whole river and was based on identifying the
flow that causes the depth at any of the shoal transects to become less than 0.6 ft within the
cross-section. The 5 percent exceedance incremental flows from the Jennings USGS gage
were used as inputs to the HEC-RAS steady-state model (see Section 3.0). Depths at each
cross-section in the river were then extracted from the model results. After inspection of these
results, a series of HEC-RAS model runs were also performed at 1 percentile increments
between the 45 and 40 percent exceedance flows, in order to determine with greater accuracy
the target MFL.
5-10
5.2 Results
Establishment of MFLs for the Alapaha River was based on the need to meet the following
requirements.
Maintain adequate physical habitat for production of macroinvertebrates with particular

concern for the following taxa: Ephemeroptera, Trichoptera, Plecoptera, and the
crayfish, Procambarus spiculifer, which is a preferred prey species of the Suwannee
Bass and a secondary prey item for largemouth bass (Wheeler and Alllen, 2003).
Maintain adequate physical habitat for those fish species that require higher velocities.
Fish likely to have higher velocity requirements were represented by the darters (Family
Percidae). Protection of habitat for darters is also important because, as possible hosts
for the glochidial larval stage, they may represent a critical path in the life stage of rare,
threatened or endangered species of unionid mussels (Georgia Museum of Natural
History, 2006). Gore et al. (2001) have suggested that, because so little is known about
the specific habitat requirements of all life stages of these mussels, that the protection of
habitat needed to support the larval hosts may be appropriate;
Ensure and maintain sufficient depth in the river to permit fish passage over shoal
habitats in the upper and lower Alapaha.
Ensure that the historical timing and duration of hydrologic connectivity between upper
and lower reaches of the Alapaha River, and the Alapaha and Suwannee, is maintained.
The maintenance of the historic regime is desirable to permit fish passage, facilitate
gene flow between different subpopulations of fish and macroinvertebrates, and allow
aquatic drift to contribute to the translocation of macroinvertebrate biomass.
Three approaches were employed to evaluate the above requirements:
Wetted perimeter analysis
Ecosystem Function Model, (EFM), and
Minimum depth for fish passage analysis.
5.2.1 Wetted Perimeter Results
Estimates of wetted perimeter were calculated for each of the 11 HEC-RAS transects above
river mile 18 (cf. Figure 5-4). Two of these transects, at river miles 19.3 and 19.93, were
chosen to evaluate the MFL. These were the transects, which showed, upon visual inspection,
the greatest degree of inflection, among transects, in wetted perimeter as flows decrease. At
each transect, a clear inflection point (Figure 5-6) demarcates critical flows at:
115 cfs at river mile 19.3 and

120 cfs at river mile 19.93.
5-11
Figure 5-6. Plots of wetted perimeter vs. flow at river miles 19.3 and 19.93 in the Alapaha River.
Flows above 115 to 120 cfs show there is no appreciable gain in wetted perimeter. At flows less
than 115 cfs there is a distinct drop-off in the amount of wetted perimeter. The assumption is
that it is of maximum benefit to the biota (e.g., fish and their macroinvertebrate prey) to have a
larger, rather than a smaller wetted perimeter. Therefore, flows of at least 115 cfs are protective
of the biota with respect to maximizing wetted perimeter.
5.2.2 EFM Results
The Ecosystem Functions Model results indicated that a suitable MFL for the Alapaha River
ranges between 100 and 110 cfs (Figure 5-7). Figure 5-7 shows that at a flow of 110 cfs there
is 12% of the habitat in the upper reach of the Alapaha River which is adequate from the
standpoint of preserving depths >2 feet and velocities >0.5 feet second-1. Below 110 cfs there is
a marked downward inflection in available habitat. Solving for the flow which corresponds to an
increased risk of up to a 15% loss in available habitat yields a critical flow of 103 cfs:
12% potential habitat at 110 cfs 10.2% potential habitat at 103 cfs = 1.8% loss, overall.
When this value is normalized to the local maximum, within the critical flow range:
1.8%/12% = 15%.
The results from the Ecosystem Functions Model indicate that a flow of at least 103 cfs is
protective of habitats preferred by the target biota for the upper Alapaha River. This includes
macroinvertebrates that are primary prey for riverine fishes, as well as fishes that may serve as
hosts for mussel larvae (i.e., habitats where velocities >0.5 feet second-1 and depths of at least
two feet (cf. Table 5-1)).
5-12
Figure 5-7. Summary of Ecosystem Function Model results for the Alapaha River protective of a 2.0-foot
water depth and a stream velocity of 0.5 feet sec-1 at the 80th percent exceedance Suwannee River stage.
5.2.3 Minimum Fish Passage Results
Water depths of at least 0.6 feet are considered sufficient to permit upstream and downstream
movements of fish populations. This criterion was used to evaluate fish passage under both
low-flow and mid-flow conditions. The low-flow evaluation only applies to the reach of the
Alapaha River above river mile 18, while the mid-flow evaluation is applicable to the entire river.
To evaluate this criterion in the upper reach of the Alapaha River, modeled depths at the shoals
transects at river miles 18.48, 18.5, 21.72, 21.74, and 21.76, were estimated as a function of
flow. Each transect was found to maintain a depth of greater than 0.6 ft at some portion of the
river channel along the cross-section at least 40% of the transect width at flows >100 cfs (Figure
5-8). The most downstream transect, at river mile 18.48, met the 0.6 foot criterion at least 67%
of the transects linear distance at flows >100 cfs. Therefore, the MFL estimates generated by
wetted perimeter and EFM analyses also protect fish passage requirements.
The model results also supported a mid-flow MFL at the Jennings gage ranging between 675
cfs (45th percent exceedance flow) and 843 cfs (40 percent exceedance flow). A mid-flow MFL
5-13
was deemed appropriate due to the capture of low flows by the swallets located in the upper
reach of the Alapaha River. When flows are below the ~500 cfs threshold identified in Chapter
3, the Dead River and swallets located below SR 150 capture low flows in the underlying
aquifer. The result is a drying out of the Alapaha in the lower reaches of the river. At flows
above 500 cfs, the aquifer is saturated and the river channel becomes wetted once more and
flows resume throughout the river. The importance of a mid-flow MFL is that it ensures
connectivity between local populations of fish in the Alapaha River and larger populations of fish
in the Suwannee River, and hence promotes genetic variation amongst the entire population.
A second set of HEC-RAS model runs was made to determine the target MFL with greater
resolution. Model estimates were obtained at 1% exceedance flow increments using the
aforementioned 675 cfs 843 cfs range of flows. Model results demonstrated that the mid-level
MFL should be 800 cfs (the 41 percent exceedance flow). This flow was determined to be
critical because at flows below 800 cfs, the 0.6 ft fish passage criterion is not ensured
throughout the lower reach of the Alapaha River. At this flow, the river channel at river mile
10.01 is the final downstream cross-section to become sufficiently inundated (i.e., at least some
portion of the river channel has a depth of the water column greater than or equal to a critical
depth) to depths greater than 0.6 feet. Therefore, the 800 cfs threshold flow is the minimum
flow necessary to permit fish passage throughout the entire Alapaha River reach and maintains
longitudinal connectivity throughout the river.
Based upon the 0.6 foot fish passage criterion, flows of at least 100 cfs will meet the minimum
depth for fish passage at least 67% of the transect width at the most downstream shoal transect
in the upper Alapaha (river mile 18.48). Under mid-level flows, at least 800 cfs is required to
ensure fish passage throughout the river.
5-14
Figure 5-8. Fish passage (% of shoal habitat with a minimum depth greater than 0.6 feet) as a
function of flow in the upper Alapaha River.
5-15
5.3 Recommended MFLs
Three separate approaches produced low-flow MFLs for the Alapaha River ranging from 100 to
120 cfs on the portion of the river above river mile 18. The results from the wetted perimeter and
the Ecosystem Functions Model analyses were more protective than the results from the
minimum fish passage analysis.
A second MFL for mid-level flows is also proposed. This mid-level MFL satisfies the
requirements for fish passage over several shoals in the lower Alapaha River and maintains the
historic connectivity regime between the Alapaha River and the Suwannee River. Conceptually,
the establishment of a mid-range flow MFL of 800 cfs for the Alapaha River is to be interpreted
as follows: a decrease in the frequency of flows at 800 cfs of 15% from historically-observed
flow frequency is the maximum allowable deviation from baseline levels. Thus, the change in
frequency of mid-range flow MFL is calculated as follows:
41% exceedance flow x 15% allowable decrease in frequency = 6.2% change in frequency
41% exceedance flow 6.2% change in frequency = 35% MFL-adjusted exceedance flow.
Furthermore, in observance of the low-flow MFL of 115 cfs, this shift will not be allowed at flows
below this level; thus, the low-flow MFL functions as an anchor point on the MFL-adjusted
flow-duration curve. The establishment of a mid-range flow MFL of 800 cfs thus yields two
points on the flow duration curve, which must be maintained in accordance with the MFL. This
shift is observed in the Figure 5-9 and summarized Table 5-2.
Based on the weight of evidence, the proposed minimum flows are as follows:
low-flow MFL is 115 cfs.

mid-level MFL is 800 cfs.
5-16
Figure 5-9. Flow duration curves representing historic conditions and the proposed MFL
flow duration curve, with reference lines shown at 800 cfs (mid-range flows) and 115 cfs
(low flow).
Table 5-2. Percentile distributions of the Baseline and proposed MFL flow duration curves (FDCs)
(Figure 5-9).
Baseline FDC Proposed MFL FDC Difference

Percentiles (cfs) (cfs) (Maximum potentially available water)
P05 74 74 0
P10 96 96 0
P25 178 165 13
P50 543 419 124
P75 1750 1232 518
P90 3816 2686 1130
P95 5827 4102 1725
5-17
TAB 6
6.0 SUMMARY AND MFL RECOMMENDATIONS
6.1 Alapaha River Study Area
The Alapaha River is a scenic and relatively undeveloped river within Florida. The reach within
Florida has several interesting characteristics that add to its importance. Upstream of State
Route (SR) 150 (Figure 1-1b), the river is perennial and incised into a scenic, rock-bound
channel. Approximately three miles downstream from the SR 150 bridge, the river enters a
reach characterized by sinkholes that capture much of the flow during moderate- to low-flow
conditions. As a result, the majority of the river bed in Florida is dry much of the time.
Discharge of water captured by the sinkholes is through two large springs that discharge into
the Suwannee River. These springs (Alapaha Rise and Holton Rise and Creek) support
discharge and ecological values in the Suwannee River.
The Alapaha River can be characterized as a southeastern coastal plain, blackwater stream
which originates in the coastal plain of Georgia, west of the Okefenokee Swamp. The total
length of the river is 130 miles, of which 22.6 miles are located in Florida. The majority of the
Alapaha River Basin, which comprises 1840 square miles, is located in Georgia.
The Florida portion of the river flows over karstic limestone, and under low to moderate flow
conditions, river flow is captured by a series of sinkholes within the streambed. The Alapaha
River is also known as the River of Sand for this reason. The water travels underground via
caverns and conduits, then discharges from springs along the Suwannee River, most notably
the Alapaha Rise and Holton Creek Rise. These are first and third magnitude springs,
respectively (Ceryak et al., 1983).
National Wetland Inventory data show most of the riverine habitat as palustrine forested, with
limited patches of palustrine emergent vegetation. Land use data show adjacent forests as
being primarily temperate hardwoods, with few areas of managed pine plantation and oak-pine-
hickory forests. Based on the 10 year floodplain, a sizable forested floodplain exists adjacent to
the Alapaha River which is generally categorized as seasonally flooded, with northern most
portions being described as temporarily flooded. However, due to the steep gradient and incised
channels in the river, riparian vegetation adjacent to the river is generally temperate hardwoods
and improved pasture (SRWMD 1995 land use coverage), neither of which is related to
floodplain inundation. On the Alapaha, regularly inundated wetlands or swamps, such as those
that typically form headwaters or those wetlands adjacent to less incised rivers, are lacking.
6.2 MFL Evaluation Procedure
The evaluations performed for the establishment of MFLs for the Upper Santa Fe River were
conducted with the following approach:
1. Compile all best available information relative to the water bodies;

2. Evaluate the ten specific water resource values (62-40, F.A.C.) for applicability to the
water body in light of the potential for impact and the available data;
3. Evaluate the available information to determine the relationships between flow and/or
level and the water resource or related ecology;
4. Identify the limiting target value(s) that, if protected from significant adverse impact, will
protect all other potentially applicable criteria;
6-1
5. Recommend an MFL that will protect the water resource and related ecology from
significant impact; and
6. Re-evaluate the ten specific water resource values to ensure potentially applicable
values are sufficiently protected from significant risk.
6.3 MFL Evaluation Summary
As presented in Section 1, the following three values were identified as potentially limiting
conditions:
1. Fish and wildlife habitats and the passage of fish;

2. Maintenance of freshwater storage and supply;
3. Water quality.
Based on a relative impact ranking, data availability, and professional judgment, fish and wildlife
habitats and the passage of fish was selected as the critical value that, if protected, would be
most likely to protect the other potentially applicable criteria. As discussed in Sections 3 and 5,
the Baseline FDC was developed using the period of record data (measured and synthesized)
and represent conditions upon which the MFL FDC was established. Unless the historic data
upon which the MFLs were based change, the Baseline FDC remains unchanged as permitting
proceeds. The MFL FDC is developed to represent the MFL, or significant impact, for the water
body.
The development of an MFL for the Alapaha River based on the value of habitat was predicated
on the need to:
Maintain adequate physical habitat for production of macroinvertebrates with particular

concern for the following taxa: Ephemeroptera, Trichoptera, Plecoptera, and the
crayfish, Procambarus spiculifer, which is a preferred prey species of the Suwannee
Bass and a secondary prey item for largemouth bass (Wheeler and Allen, 2003).
Maintain adequate physical habitat for those fish species that require higher velocities.
Fish anticipated to have higher velocity requirements were represented by the darters
(Family Percidae). Protection of habitat for darters is also important because, as
possible hosts for the glochidial larval stage, they may represent a critical path in the life
stage of rare, threatened or endangered species of unionid mussels (Georgia Museum
of Natural History, 2006). Gore et al. (2001) have suggested that, because so little is
known about the specific habitat requirements of all life stages of these mussels, that the
protection of habitat needed to support the larval hosts may be appropriate;
Ensure and maintain sufficient depth in the river to permit fish passage over shoal
habitats in the upper and lower Alapaha.
Ensure that the historical timing and duration of hydrologic connectivity between upper
and lower reaches of the Alapaha River, and the Alapaha and Suwannee, is maintained.
The maintenance of the historic regime is desirable to permit fish passage, facilitate
gene flow between different subpopulations of fish and macroinvertebrates, and allow
aquatic drift to contribute to the translocation of macroinvertebrate biomass.
Three types of analyses were performed to determine which would be the most conservative
protector of the water resource values. An analysis was performed using the wetted perimeter
approach as an estimate of the amount of habitat available to aquatic organisms under different
6-2
flow conditions. Fish passage analysis was used to determine the minimum flow necessary to
allow 0.60 feet for fish passage through the most restrictive cross sections of the river. The
Ecological Functions Model (EFM) was utilized to evaluate the minimum flow necessary protect
instream habitat conditions. The conclusions from the three types of analyses are summarized
below:
1. The Ecosystem Functions Model results proved to be the most conservative protector
from significant ecological risk to the target biota, upstream of the capture zone near
the SR 150 bridge. The EFM results suggest a low flow MFL of 115 cfs as measured at
the Jennings USGS gage is protective of habitats preferred by the target biota.
2. A second MFL for mid-level flows is also proposed at 800 cfs. This mid-level MFL
satisfies the requirements for fish passage over several shoals in the lower Alapaha
River and maintains the historic connectivity regime between the Alapaha River and the
Suwannee River.
3. The wetted perimeter analysis results were less critical than the EFM and fish passage
results for the Alapaha River.
6.4 Recommended MFLs
6.4.1 Proposed MFL for the Alapaha River at Jennings
Table 6-1 and Figure 6-1 presents the baseline and proposed MFL FDCs for the Alapaha River
at Jennings. In observance of the low flow MFL of 115 cfs, a shift will not be allowed at flows
below this level; thus, the low flow MFL functions as an control point on the MFL-adjusted flow-
duration curve. The establishment of a mid-range flow MFL of 800 cfs thus yields two control
points on the flow duration curve,. Conceptually, the establishment of a mid-range flow MFL of
800 cfs for the Alapaha River should be interpreted as follows: a decrease in the frequency of
flows at 800 cfs of 15% from historically-observed flow frequency is the maximum allowable
deviation from baseline levels.
Table 6-1. Comparison of Proposed Baseline and MFL FDCs for the Alapaha River at Jennings.
Difference
Baseline FDC Proposed MFL FDC
Percentiles (Maximum potentially
(cfs) (cfs)
available water)
P05 74 74 0
P10 96 96 0
P25 178 165 13
P50 543 419 124
P75 1750 1232 518
P90 3816 2686 1130
P95 5827 4102 1725
6-3
Figure 6-1. Comparison of Baseline and proposed MFL flow duration curves for the Alapaha
River flow at the Jennings gage.
6-4
Appendices
Appendix 4-A: Additional Water Quality Plots
Alapaha River
Suwannee River Water Management District
XXX
Alapaha River Basin
XXX
Water Temperature Mean Annual Water Temperature
(C)
30
25
20
15
10
0
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Conductivity Mean Annual Conductivity
(umhos/cm)
10050
9550
9050
8550
8050
7550
7050
6550
6050
5550
5050
4550
4050
3550
3050
2550
2050
1550
1050
550
50
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
PH Mean Annual PH
(Standard Units)
14
12
10
4
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Alkalinity Mean Annual Alkalinity
(mg/L)
265
235
205
175
145
115
85
55
25
-5
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Color Mean Annual Color
(Platnum Cobalt Units)
710
660
610
560
510
460
410
360
310
260
210
160
110
60
10
-40
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Turbidity Mean Annual Turbidity
(NTU)
30
25
20
15
10
-5
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Total Suspended Solids Mean Annual Total Suspended Solids
(mg/L)
25
20
15
10
-5
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
XXX
Alapaha River Basin
XXX
Total Organic Carbon Mean Annual Total Organic Carbon
(mg/L)
90
75
60
45
30
15
0
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Total Kjeldahl Nitrogen Mean Annual Total Kjeldahl Nitrogen
(mg/L)
10
-2
1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Ammonia Mean Annual Ammonia
(mg/L)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
-0.1
-0.2
-0.3
-0.4
-0.5
-0.6
-0.7
-0.8
-0.9
-1.0
1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Nitrate+Nitrite Mean Annual Nitrate+Nitrite
(mg/L)
1.45
1.15
0.85
0.55
0.25
-0.05
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Total Nitrogen Mean Annual Total Nitrogen
(mg/L)
129
119
109
99
89
79
69
59
49
39
29
19
-1
1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Total Phosphorous Mean Annual Total Phosphorous
(mg/L)
4
-1
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
XXX
Alapaha River Basin
XXX
Orthophosphate Mean Annual Orthophosphate
(mg/L)
1.2
1.1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
-0.1
-0.2
-0.3
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Appendix 4-B: List of Fish Species Reported in the Suwannee Drainage
Compiled from Hellier (1967) and Bass (1991)
Appendix 4-B
List of Fish Species Reported in the Suwannee Drainage Compiled from Hellier (1967) and Bass (1991)
Family Genus Species Common Name Reference River/Drainage

Lepisosteidae Lepisosteus platyrhincus Florida spotted gar Hellier '67; Santa Fe
Lepisosteidae Lepisosteus platyrhincus Florida spotted gar Bass in Livingston '91 Suwannee
Amiidae Amia calva bowfin Hellier '67 Santa Fe
Amiidae Amia calva bowfin Bass in Livingston '91 Suwannee
Umbridae Umbra pygmaea eastern mudminnow Hellier '67 (UF collec.) Santa Fe
Umbridae Umbra pygmaea eastern mudminnow Bass in Livingston '91 Suwannee
Esocidae Esox americanus redfin pickerel Hellier '67 Santa Fe
Esocidae Esox americanus redfin pickerel Bass in Livingston '91 Suwannee
Esocidae Esox niger chain pickerel Hellier '67 Santa Fe
Esocidae Esox niger chain pickerel Bass in Livingston '91 Suwannee
Cyprinidae Notemigonus crysoleucas golden shiner Hellier '67 Santa Fe
Cyprinidae Notemigonus crysoleucas golden shiner Bass in Livingston '91 Suwannee
Cyprinidae Notemigonus chalybaeus ironcolored shiner Hellier '67 Santa Fe
Cyprinidae Notemigonus chalybaeus ironcolored shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis emiliae pugnose minnow Hellier '67 and UF collec. Santa Fe
Cyprinidae Notropis emiliae pugnose minnow Bass in Livingston '91 Suwannee
Cyprinidae Notropis harperi redeye chub Hellier '67 Santa Fe
Cyprinidae Notropis harperi redeye chub Bass in Livingston '91 Suwannee
Cyprinidae Notropis hypselopterus sailfin shiner Hellier '67 Santa Fe
Cyprinidae Notropis hypselopterus sailfin shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis leedsi bannerfin shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis maculatus taillight shiner Hellier '67 Santa Fe
Cyprinidae Notropis maculatus taillight shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis petersoni coastal shiner Hellier '67 Santa Fe
Cyprinidae Notropis petersoni coastal shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis texanus weed shiner Bass in Livingston '91 Suwannee
Cyprinidae Notropis venustus blacktail shiner Bass in Livingston '91 Suwannee
Cyprinidae Semotilus atromaculatus creek chub Bass in Livingston '91 Suwannee
Catostomidae Erimyzon sucetta lake chubsucker Hellier '67 Santa Fe
Catostomidae Erimyzon sucetta lake chubsucker Bass in Livingston '91 Suwannee
Catostomidae Minytrema melanops spotted sucker Hellier '67 Santa Fe
Catostomidae Minytrema melanops spotted sucker Bass in Livingston '91 Suwannee
Ictaluridae Ictalurus catus white catfish Hellier '67 Santa Fe
Ictaluridae Ictalurus natalis yellow catfish Hellier '67 Santa Fe
Ictaluridae Ictalurus natalis yellow catfish Bass in Livingston '91 Suwannee
Ictaluridae Ictalurus nebulosus marmoratus brown bullhead Hellier '67 Santa Fe
Ictaluridae Ictalurus nebulosus brown bullhead Bass in Livingston '91 Suwannee
Ictaluridae Ictalurus punctatus channel catfish Hellier '67 Suwannee
Ictaluridae Ictalurus punctatus channel catfish Bass in Livingston '91 Suwannee
Ictaluridae Ictalurus serracanthus spotted bullhead Bass in Livingston '91 Suwannee
Ictaluridae Noturus gyrinus tadpole madtom Hellier Santa Fe
Ictaluridae Noturus gyrinus tadpole madtom Bass in Livingston '91 Suwannee
Ictaluridae Noturus leptacanthus speckled madtom Hellier '67 Santa Fe
Ictaluridae Noturus leptacanthus speckled madtom Bass in Livingston '91 Suwannee
Aphredoderidae Aphredoderus sayanus pirate perch Hellier '67 Santa Fe
Aphredoderidae Aphredoderus sayanus pirate perch Bass in Livingston '91 Suwannee
Fundulidae Fundulus chrysotus golden topminnow Hellier '67 Santa Fe
Fundulidae Fundulus chrysotus golden topminnow Bass in Livingston '91 Suwannee
Fundulidae Fundulus cingulatus banded topminnow Hellier '67 Santa Fe
Fundulidae Fundulus cingulatus banded topminnow Bass in Livingston '91 Suwannee
Fundulidae Fundulus escambiae eastern starhead topminnow Bass in Livingston '91 Suwannee
Fundulidae Fundulus lineolatus lined topminnow Bass in Livingston '91 Suwannee
Fundulidae Fundulus notti starhead topminnow Hellier '67 Santa Fe
Fundulidae Fundulus seminolis seminole killifish Hellier '67 Santa Fe
Fundulidae Fundulus seminolis seminole killifish Bass in Livingston '91 Suwannee
Fundulidae Jordanella floridae flagfish Hellier '67 Santa Fe
Fundulidae Jordanella floridae flagfish Bass in Livingston '91 Suwannee
Fundulidae Leptolucania ommata pygmy killifish Hellier '67 Santa Fe
Fundulidae Leptolucania ommata pygmy killifish Bass in Livingston '91 Suwannee
Fundulidae Lucania goodei bluefin killifish Hellier '67 Santa Fe
Fundulidae Lucania goodei bluefin killifish Bass in Livingston '91 Suwannee
Poeciliidae Gambusia affinis mosquitofish Hellier '67 Santa Fe
Poeciliidae Gambusia affinis mosquitofish Bass in Livingston '91 Suwannee
Poeciliidae Heterandria formosa least killifish Hellier '67 Santa Fe
Poeciliidae Heterandria formosa least killifish Bass in Livingston '91 Suwannee
Poeciliidae Poecilia latipinna sailfin mollie Hellier '67 Santa Fe
Poeciliidae Poecilia latipinna sailfin mollie Bass in Livingston '91 Suwannee
Atherinidae Labidesthes sicculus brook silverside Bass in Livingston '91 Suwannee
Centrarchidae Acantharchus pomotis mud sunfish Bass in Livingston '91 Suwannee
Centrarchidae Centrarchus macropterus flier Hellier '67 Santa Fe
Centrarchidae Centrarchus macropterus flier Bass in Livingston '91 Suwannee
Centrarchidae Elassoma evergladei Everglades pygmy sunfish Hellier '67 Santa Fe
Centrarchidae Elassoma evergladei Everglades pygmy sunfish Bass in Livingston '91 Suwannee
Centrarchidae Elassoma okefenokee Okeefenokee pygmy sunfish Hellier '67 Santa Fe
Centrarchidae Elassoma okefenokee Okeefenokee pygmy sunfish Bass in Livingston '91 Suwannee
Centrarchidae Elassoma zonatum banded pygmy sunfish Hellier '67 Santa Fe
Centrarchidae Elassoma zonatum banded pygmy sunfish Bass in Livingston '91 Suwannee
Centrarchidae Enneacanthus chaetodon blackbanded sunfish Bass in Livingston '91 Suwannee
Centrarchidae Enneacanthus gloriosus bluespotted sunfish Hellier '67 Santa Fe
Centrarchidae Enneacanthus gloriosus bluespotted sunfish Bass in Livingston '91 Suwannee
Centrarchidae Enneacanthus obsesus banded sunfish Hellier '67 (UF collec.) Santa Fe
Centrarchidae Enneacanthus obsesus banded sunfish Bass in Livingston '91 Suwannee
Centrarchidae Lepomis auritus redbreast sunfish Hellier '67 Santa Fe
Centrarchidae Lepomis auritus redbreast sunfish Bass in Livingston '91 Suwannee
Centrarchidae Lepomis gulosus warmouth Hellier '67 Santa Fe
Centrarchidae Lepomis gulosus warmouth Bass in Livingston '91 Suwannee
Centrarchidae Lepomis macrochirus bluegill Hellier '67 Santa Fe
Centrarchidae Lepomis macrochirus bluegill Bass in Livingston '91 Suwannee
Centrarchidae Lepomis marginatus dollar sunfish Hellier '67 (Gilbert '61) Santa Fe
Centrarchidae Lepomis marginatus dollar sunfish Bass in Livingston '91 Suwannee
Centrarchidae Lepomis microlophus redear sunfish Hellier '67 Santa Fe
Centrarchidae Lepomis microlophus redear sunfish Bass in Livingston '91 Suwannee
Centrarchidae Lepomis punctatus spotted sunfish Hellier '67 Santa Fe
Centrarchidae Lepomis punctatus spotted sunfish Bass in Livingston '91 Suwannee
Centrarchidae Micropterus notius Suwannee bass Hellier '67 Santa Fe
Centrarchidae Micropterus notius Suwannee bass Bass in Livingston '91 Suwannee
Centrarchidae Micropterus salmoides floridanus largemouth bass Hellier '67 Santa Fe
Centrarchidae Micropterus salmoides largemouth bass Bass in Livingston '91 Suwannee
Centrarchidae Pomoxis nigromaculatus black crappie Hellier '67 Santa Fe
Centrarchidae Pomoxis nigromaculatus black crappie Bass in Livingston '91 Suwannee
Percidae Etheostoma edwini brown darter Hellier '67 Santa Fe
Percidae Etheostoma edwini brown darter Bass in Livingston '91 Suwannee
Percidae Etheostoma fusiforme swamp darter Hellier '67 Santa Fe
Percidae Etheostoma fusiforme swamp darter Bass in Livingston '91 Suwannee
Percidae Percina nigrofasciata blackbanded darter Hellier '67 Santa Fe
Percidae Percina nigrofasciata blackbanded darter Bass in Livingston '91 Suwannee
Literature Cited
MASTER LIST OF LITERATURE CITED - ALAPAHA RIVER MFL TECHNICAL REPORT
Abbott, J.R., and W.S. Judd, 1998. Floristic Inventory of the Waccasassa Bay State Preserve, Levy County,
Florida. Masters thesis submitted to the University of Florida, Department of Botany.
Allan, J. D. 1995. Stream Ecology. Structure and Function of Running Waters. Chapman and Hall, New York,
NY. 388 p.
Allison, D., M. Groszos, and F. Rupert, 1995. Top of rock of the Florida Aquifer System in the Suwannee River
Water Management District. Florida Geological Survey Open File Map Series: No. 84.
Anderson, J.R., and A.K. Morison, 1989. Environmental Flow Studies of the Wimmera River, Victoria. Part D. Fish
populations - Past, Present and Future. Conclusions and Recommendations. Arthur Rylah.
Annear, T.C., and A.L. Condor, 1984. Relative bias of several fisheries instream flow methods. North American
Journal of Fisheries Management, 4:531- 539.
Arthington, A.H., and J.M. Zalucki (eds.), 1998. Comparative Evaluation of Environmental Flow Assessment
Techniques: Review of Methods. Land and Water Resources Research and Development Corporation, Canberra,
Occasional Paper 27/98.
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TECHNICAL REPORT

Water Resource Associates, Inc.

SDII Global Janicki Environmental

3.0 HYDROLOGIC ANALYSES ..................................................................................3-1

4.0 ECOLOGICAL ANALYSES ..................................................................................4-1

6.0 SUMMARY AND MFL RECOMMENDATIONS .....................................................6-1

Figure 1-1a. Total extent of the Alapaha drainage basin. .......................................................1-3

Figure 2-1 Suwannee River Basin in Florida and Georgia.

Figure 4-1 Locator map of the Alapaha River in Florida showing

Figure 5-1 Examples of a stream cross-section (top) and the

Table 1-1 MFL Decision Matrix: Alapaha River .................................................................1-9

Table 2-1 Descriptive data on the Suwannee

Table 4-1 List of fish species recorded in the Georgia

Proposed MFL for the Alapaha River at Jennings

To satisfy the requirement of state water law and policy.

1.1 State of Florida Law Pertaining to the Establishment of MFLS

Chapter 373.042, Florida Statutes (F.S.) specifies that:

a) Recreation in and on the water;

1.3 Water Body Regulatory Designations

Figure 1-1a. Total extent of the Alapaha drainage basin.

Alapaha River Jasper

Suwannee River Major Roads

1.4 Relevant Environmental and Water Resource Values

1.4.1 Method of Identification of Relevant Environmental and Water Resource Values

Obtain All Available and Evaluate Each EWRV for

MFL DEVELOPMENT PHASE

Identify Limiting EWRV(s) That

Recommend MFLs to Avoid

h. Sediment loads. This water-resource value is considered somewhat relevant to the

Fish and wildlife habitats and the passage of fish,

Recreation in and on the water 1 2 1 4 1 Y N

Transfer of detrital material 1 1 1 3 1 Y N

2.1 Suwannee River Basin

2.1.1 Physical Setting of the Suwannee Basin

** - includes the contributions of the Withlacoochee, Alapaha and Santa Fe sub-basins

Terrace Approximate Elevation Range

The month-to-month variation in rainfall is as important to understanding the Suwannees

The uppermost geologic unit consists of the Pliocene- and Quaternary-aged

2.1.4 Regional Aquifer Systems

2.1.5 Land and Water Use in the Suwannee River Basin

2.1.5.1 Land Use and Population Characteristics

2.1.5.2 Water Use

2.2.1 Surfacewater Hydrology

2.2.1.1 Annual Yield

2.2.1.2 Spatial Flow Patterns

A. Stream hydrology - Upper Suwannee Drainage (above Cody Escarpment)

Mean Monthly Streamflow (cfs)

B. Stream hydrology - Lower Suwannee Drainage (below Cody Escarpment)

Mean Monthly Streamflow (cfs)

2.2.1.3 Seasonal Flow Patterns

Temporal patterns in discharge are also affected by geologic characteristics. Downgradient of

2.2.1.4 Tidal River and Estuary

2.2.1.5 Chemical Characteristics

Reach 1. Upper River Blackwater Reach 4. Lower River Calcareous

Reach 1 Reach 2 Reach 3 Reach 4 Reach 5

2.2.2.1 Aquatic and Wetland Communities

Southeastern Plains Ecoregion

Southern Coastal Plain Ecoregion

2.2.2.2 River Reach Ecology

2.2.2.2.1 Suwannee River Mainstem

2.2.2.2.2 Santa Fe River

2.2.2.2.3 Withlacoochee River

2.2.2.2.4 Alapaha River