Indian River Lagoon

Numerical Model Flushing Experiments

(Draft)

Submitted to the
St. Johns River Water Management District
4049 Reid Street
Palatka, FL 32177

Gary A. Zarillo, Ph.D., PG

Florida Institute of Technology
Melbourne, FL
321 794-3398
zarillo@fit.edu

April 27, 2015

Executive Summary
In order to examine the potential for improved flushing of the Indian River Lagoon (IRL)
U.S. Army Corps of Engineers Coastal Modeling System (CMS) was used for hydrodynamic and
transport modeling. The CMS is an integrated 2D numerical modeling system for simulating
circulation, water level, constituent transport, sand transport, and morphology change in shallow
water environments. For this project, two computational model grids were constructed to cover
the Indian River Lagoon System from the north end of the Mosquito Lagoon (ML) in Volusia
County. FL to the Wabasso area of Indian River County. The north grid (Grid 1) includes the
Mosquito Lagoon and the north compartment of the Indian River Lagoon (IRL) The south grid
(Grid 2) includes the Banana River and the IRL from the Cocoa area to Wabasso. A uniform grid
resolution of 50 was found to provide adequate spatial resolution and numerical stability. The
model boundaries were forced with historical time series of water level and with discharge at
major creeks and rivers entering the west bank of the IRL. Wind speed and direction were
applied over the surface of the model grid.
A total of seven model runs were conducted, including two runs to simulate existing
conditions. Model performance was validated by comparing predicted and measured water level
time series. Five model runs included hypothetical new tidal inlets, pumping stations, and
hypothetical widening of Sebastian inlet near the south boundary of Grid 2. Flushing rates were
predicted by establishing an initial numerical tracer concentration of 20 parts per thousand over
the entire model domain. Tracer concentrations at the model boundaries were then set to zero.
Model results for existing conditions were consistent with previous studies by showing
that the southern portion of the Mosquito Lagoon and the Banana River remain poorly flushed
over long periods of time. The Titusville area of the IRL also remained poorly flushed in model
simulations of existing conditions. Among the hypothetical alterations to the model grids,
additional tidal inlet and pumping station connections to the coastal ocean across narrow sections
of the barrier island, produced the best flushing results in the model grids. Either a narrow tidal
inlet or pumping station located in the south compartment of the Mosquito Lagoon produced
complete flushing of the ML and north compartment of the IRL (Grid 1) within about 70 days or
less. A tidal inlet across the South Cocoa Beach barrier island segment also substantially
improved flushing of the Banana River. Opening the water locks at Port Canaveral also
improved flushing, but at a somewhat slower rate to the tidal inlet case. This is attributed to the
long conveyance channel between the Port entrance and the Banana River, which may dissipate
tidal energy to a greater degree. Widening of Sebastian Inlet to twice its present width at the
throat section did not noticeably improve flushing rates or extent

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Table of Contents
Executive Summary ........................................................................................................................ ii
Introduction and Goals ................................................................................................................... 1
Model Features............................................................................................................................ 1
Model Setup .................................................................................................................................... 2
Grid Generation .......................................................................................................................... 2
Wind Time Series ....................................................................................................................... 5
Model Validation ............................................................................................................................ 5
Model Runs ..................................................................................................................................... 7
Model Results ................................................................................................................................. 8
Model Run1 Predicted Flushing, North Grid.............................................................................. 8
Model Run 2; Predicted Flushing, South Grid............................................................................ 9
Model Run 3: Tidal Inlet, Mosquito Lagoon ............................................................................ 10
Model Run 4: Pumping Station, Mosquito Lagoon .................................................................. 12
Model Run 5: Tidal Inlet South Cocoa Beach ....................................................................... 13
Model Run 6: Canaveral Locks Open ....................................................................................... 14
Model Run 7: Widening of Sebastian Inlet............................................................................... 16
Conclusions ................................................................................................................................... 17
References ..................................................................................................................................... 18

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Introduction and Goals

Preliminary model circulation experiments were performed in 2013 that involved
structural modification of the Indian River Lagoon geometry. These included adding a small
tidal, a pump station, and hypothetical widening of Sebastian Inlet. This exercise showed that
some influence on tidal circulation and tidal amplitude would occur within the Indian River
Lagoon compartment around Sebastian Inlet. This exercise applied the 2-dimensional coastal
Modeling System (CMS) developed by the Coastal hydraulics Laboratory for use in shallow
coastal areas.
In the present project, the earlier work is expanded to examine flushing rates in the north
and central Indian River Lagoon compartments and the Mosquito Lagoon. Hypothetical inlets
and pumping station canals were added to the IRL at selected locations, along with model tests
involving widening of Sebastian Inlet and opening of the water locks within the interior of port
Canaveral. Although CMS is capable of including wave propagation, sediment transport, and
morphologic change over time, model tests were restricted to simulation of flushing times
without considering potential consequences of modification of IRL geometry on processes like
wave-driven littoral drift, shoal building, and regional sediments budgets.
The goal of applying numerical tests of flushing rates in the north and central IRL, is to
identify the potential for improving the state of water qualify by promoting more rapid
exchanges with the coastal ocean. Although the likely side effects of promoting exchanges in
terms of morphodynamics are not considered in this project, model forcing was kept as real as
possible by including real time series of water elevation and discharge inflows at model
boundaries.
Model Features
The Coastal Modeling System (CMS) was developed by the U.S. Army Engineer
Research and Development Center (ERDC), Coastal and Hydraulics Laboratory (CHL). CMS is
a coupled group of numerical models for calculating waves, circulation, sediment transport,
constituent transport, and morphology change. Calculations can be performed for flows
generated by tide, wind, waves, river discharges, and changes in salinity. A significant study for
model verification and validation of the CMS is documented in Demirbilek (2011), Lin (2011),
Sanchez (2011a) and Sanchez (2011b). Further documentation of the CMS including processes
and numerics are documented in Wu (2010) and Buttolph (2006).
CMS-Flow is a 2-D finite-volume model that solves the mass conservation and shallowwater momentum equations of water motion. CMS-Flow is forced by water surface elevation
(e.g., from tide), wind and river discharge at the model boundaries, and wave radiation stress and
wind field over the model computational domain.
CMS-Flow is presently capable of 2-D transport computations in both the explicit and
implicit solvers. The simulation of constituent transport can often require a three-dimensional (3D) solution due to the presence of vertical gradients that can influence the flow. It is therefore
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important to understand the limitations of 2-D transport simulations, and apply them only when
the assumptions inherent in 2-D simulations are valid. Typically, 2-D salinity simulations are
valid in a well mixed the water column. These conditions are usually met for shallow bays with
open exchanges to the ocean or gulf, and strong tidal signals and sufficient wind energy to
provide the vertical mixing. Thus it is assumed that the Indian River Loon system is largely well
mixed in the vertical and over time scales of the computations performed in the study, which are
the order of 1 year.

Model Setup
Grid Generation
Two model grids were constructed, one covering the Mosquito lagoon and the north
compartment of the Indian River Lagoon (IRL. The second grid included Indian River lagoon
compartments between Titusville and the Wabasso area of north Indian River County, FL.
Having two model grids facilitated shorter computational run times and more model tests
running on several computers. Model grids resolution was set at 50 meters and both grids were
generated in the AquaveoTM Surface Water Modeling System (SMS) Platform. Figure 1
illustrates the north grid and Figure 2 shows the south grid.
Figure 3 shows the available monitoring data assembles though the efforts of the St.
Johns River Water Management District (SJRWMD). In general the monitoring time series
covers the period between 1996 and 2006. Some data sets extend through 2006. The boundaries
of the two model grids were set to correspond to available water level time series and in some
cases discharge time series.

Figure 1. Configuration of Model Grid 1 (north grid)

Figure 2. Configuration of Model Grid 2 (south grid)

Boundary Water Level and Discharge Time series

For the existing condition model runs over the north grid (Figure 1) water level boundary
conditions were set at the north end of the mosquito lagoon (mosquito) and at the Titusville
bridge station (titubrew, Figure 3). The time period represented for the Grid 1 model run is 1999
since the station records included very few data gaps. Time series of water level and discharge
from Turnbull Creek were not included since the data records from this station ended in March
1998. Discharges from the District HSPF watershed sub-basin model were not included since
they are predicted, very small, and distributed over a large area. The selected model time period
for Grid 2 (North IRL to Wabasso area) is 1997, which includes the most complete time series of
data for boundary conditions. Discharge time series were applied at the Eau Gallie, River, Crane
Creek, Turkey Creek, in the Sebastian River where the gauged discharges from the S-157
structure and the Fellsmere Canal were combined. Figure 4 shows model details around the
Sebastian area including water level and discharge inputs at CMS boundary cell strings.

Figure 3. Location of monitoring stations throughout the north and central Indian River Logoon.

Wind Time Series

CMS flow will assimilate wind data as multiple inputs over selected cells or as global
input over the entire model domain. In this study three wind records were applied, The wind
record (1999) applied to Grid 1 was taken from the Pone de Leon Inlet (poneinl , Figure 3)
metrological station including globally for over Grid 1. Wind records applied to Grid 2 (1997)
were taken from the Banana River and Ft. Pierce Inlet metrological stations (See Figure 3)

Figure 4. Model grid detials and boundary conditions in the Sebastian Inlet area

Model Validation
Two data records were used to validate model predictions relative to water elevation. A
portion of the 1999 water level record from Haulover Canal (Station Haulover, Figure 3) was
compared to predicted water levels at e same location. Figure 5 shows time series of measured
and model data at the Haulover Canal station. The R-square value of 0.90 refers to a bivariate
comparison of the data. Similar to calibration results for the hydrological and water quality mode
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of the Mosquito Lagoon (Zarillo et al, 2010) the best fit between measured and model data was
found when the mean elevation north boundary water level time series was set down by 15 cm (0.15m)

Figure 5. Model and measured water level comparison at Haulover Canal

Water level predictions on Grid 2 (south grid) were compared at station spsebars (see
Figure 3) near the mouth of the Sebastian River. Figure 6 shows the comparison between
measured and model data at this location. The R-square value of 0.90 refers to a bivariate
comparison of the data. No adjustments were made to mean water level values at Sebastian Inlet
or at the Wabasso Bridge water level time series to achieve the comparison shown in Figure 6.

Figure 6. Model and measured water level comparison in the Sebastian River.

Model Runs
Table 1 lists model configuration for each of the model runs conducted in this study to
evaluate flushing conditions. Each model run began with specifying an initial tracer
concentration of 20 parts-per-thousand (ppt) throughout the model domain. Tracer concentration
at the model boundaries was set to zero though each model run. The initial year-long runs were
configured for existing conditions. Subsequent model configurations included hypothetical tidal
inlets, a one- way pumping station, a widened version of Sebastian Inlet, and opening of the
water locks to the west of Port of Canaveral entrance.
Model
Run
1
2
3
4
5
6
7

Table 1. Model Runs

Grid
Configuration

Duration

Grid 1
Grid 2
Grid 1
Grid 1
Grid 2
Grid 2
Grid 2

1999/365 days
1997/ 340 days
1999/365 days
1999/365 days
1997/ 340 days
1997/ 340 days
1997/ 340 days

Existing
Existing
ML Inlet
ML pumping station
Inlet at PAFB
Canaveral Locks Open
Widen Sebastian Inlet

Model Results
The major model results of numerical flushing experiments are presented in an electronic
appendix to this document for convenient review. The appendix includes a slide presentation
that is linked animation files. A convenient video players is also included in the electronic
appendix for convenient frame by frame viewing of the animation files that show tracer
concentrations at a daily update time scale.
Model Run1 Predicted Flushing, North Grid
Results of model flushing experiments on Grid 1 (north grid) for the existing
configuration are shown in Figures 7 and 8. The tracer concentration of 20 ppt decreased to less
than half of the initial value over the north section of the grid within about 30 days. After 150
days of simulation the predicted tracer concentrations were less than 10 ppt over about 75% of
the model domain (Figure 8A) At the end of the 365-day simulation tracer concentrations were
near zero over about 80% of the Mosquito Lagoon and the north compartment of the IRL (Figure
8B). However the south end of the ML and north end of the IRL retained high tracer
concentrations.

Figure 7. Predicted tracer concentration for Model Run 1, existing configuration at day 0 (A) and day 30
(B).

Figure 8. Predicted tracer concentration for Model Run 1 existing configuration after 150 days (A) and
365 days (B)

Model Run 2; Predicted Flushing, South Grid

Figure 9 shows predicted tracer concentrations for the existing configuration of the IRL
represented in model Grid 2. After about 150 days of simulation tracer concentrations remain
above 50% percent of the initial value of 20 ppt over more than half the model domain. After
340 days of simulation tracer concentrations over most of the model domain are reduced but
values remain well above 50% the initial 20 ppt over much of the area.

Figure 9. Predicted tracer concentration for the Model Run 2 existing configuration at day 0 (A), day
150, and day 340 (C).

Model Run 3: Tidal Inlet, Mosquito Lagoon

Model Run 3 (Table 2) over Grid 1 included an inlet scale opening across the barrier
island near the south end of Mosquito lagoon. Figure 10 shows the inlet configuration and water
elevation time series paced in the 2 boundary cells representing the inlet. In order to preserve the
calibration the same tidally influenced time series applied at the north boundary was applied
without any further adjustments to the mean water elevation. The approximate width of the inlet
is 50 meters. The refinement of 2 column of grids cells to accommodate the inlet width can be
seen in Figure 10. Figure 11 shows the depth refinement associated with the inlet channel
entering the IRL. The inlet throat as represented in the grid is 3 m deep and the conveyance
channel extending west into the IRL is 2 to 2.5 m deep

Figure 10. Location of a hypothetical tidal inlet exchange with the Atlantic Ocean across the barrier island
at south compartment of the Mosquito lagoon.

Results of the model run including the hypothetical inlet into the ML showed substantial
decrease in the time to flush the entire ML and north compartment of the IRL. Figure 12
summarizes the results and shows about 50% of the system flushed to less than half the initial
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tracer concentration within about 30 days. After 70 days of simulation tracer concentrations are
reduced to a few ppt or less over the system.

Figure 11. Details of the ML inlet channel receiving water level forcing from the coastal ocean.

Figure 12. Predicted tracer concentration for Model Run 3, ML tidal inlet after 30 days (A) and 70 days
(B)

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Model Run 4: Pumping Station, Mosquito Lagoon

Model Run 3 applied a configuration similar to that of the ML inlet. However in this run
the inlet configuration was converted to a pumping station in which a constant inflow of 100
m3/s was applied to a 50-m wide canal. The concept and dimension is similar to the engineered
canal systems that provide coastal cooling water to power plants. The canal is represented by a
grid column refinement 2-cells wide, each cell being about 25 m in width. An inflow of 50 m3/s
was specified into the seaward side of the canal as shown in Figure 13

Figure 13. Pump intake canal located in the southern compartment of the Mosquito Lagoon.

Results of the pumping station model test are similar to those of the hypothetical tidal
inlet at the same location. However the predicted rate of flushing is somewhat faster. After about
12 days of simulation half of the Mosquito lagoon is reduced to tracer concentrations below
about 5 to 10 ppt (Figure 14A) After 30 days of simulation, the entire ML basin is at a tracer
concentration of 10 ppt or less (Figure 14B After 50 days both the ML and north IRL
compartments have low remaining tracer concentrations (Figure 14C).

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Figure 14. Predicted tracer concentration for Model Case 4, pumping station located in the south
compartments of the ML (A, 12 days, B, 30 days and C, 50 days).

Model Run 5: Tidal Inlet South Cocoa Beach

Model Run 5 on Grid 2 (see table 2) includes a hypothetical tidal Inlet cut through a
narrow section of the barrier island immediately north of Patrick Air Force Base in South Cocoa
Beach. Figure 15 shows the configuration of the inlet and input water level times series. The
Sebastian Inlet water level time series was applied at the open inlet boundary without adjustment
to the mean water level in order to maintain the model validation. Inlet dimensions.

Figure 15. Location of hypothetical tidal inlet located aross the barrie island at South Cocoa Beach
(Model Run 5).

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Figure 16 summarizes the results of the Model Run 5 experiment. After 30 days of
simulation, reductions in tracer concentration can be seen in the Sebastian Inlet area and in the
and South Cocoa Beach area of the IRL. After 150 days of simulation the flushing influence of
both inlets merge and extend into the Banana River compartment of the IRL. Completion of the
model run at 340 days produces flushing effects to the north end of the Banana Rive. However,
the north compartment of the IRL included in Grid 2 does not flush. Since no water level
condition was specified at the north boundary of Grid 2 and the Canaveral barge canal extension
,was not included in the grid, the lack of flushing of this compartment just to the south of
Titusville may not be realistic.

Figure 16. Predicted tracer concentration for Model Case 5, tidal inlet located at South Cocoa beach (A 30 days, B 90 days and C, 340 days).

Model Run 6: Canaveral Locks Open

Model Run 6 includes opening of the Port of Canaveral locks for free exchange with the
Banana River as shown in Figure 17. Water Depths through the lock area were set at 3 to 5 m
and the channel width set at about 50 m. Previous work by Zarillo et al, 2014 shows that the
amplitude and phase of the tide at Sebastian Inlet is similar to that recorded at the Trident Pier
NOAA water level gauge. Therefore, to be consistent with the overall modeling effort and to
preserve the validation of the model, the measured water level time series was applied to the
entrance of Port Canaveral (Figure 17).
Figure 18 summarizes the results of hypothetical opening the Canaveral locks on flushing
of the IRL and Banana River. Predicted Tracer concentrations are shown at 30, 90 and 100 days
of simulations for comparison to the tidal inlet case shown in Figure 16. Hypothetical opening
of the Caravel locks results in flushing patens similar to that resulting from the south Cocoa
beach tidal inlet. However, the rate of flushing is slower by comparison and the final result after
340 days of simulation, leaves higher tracer concentrations at the north end of the Banana River.
The slower pace of flushing in the Canaveral Lock case is most likely due to the longer
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conveyance channel across Cape Canaveral compared to the length of the inlet across the barrier
island at South Cocoa Beach.

Figure 17. Configuration of Model Run 7, hypothetical opening of the Port of Canaveral water locks

Figure 18. Predicted tracer concentration for Model Case 5, Canaveral locks open (A - 30 days, B 90
days and C, 340 days).

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Model Run 7: Widening of Sebastian Inlet

Figure 19 shows the configuration of hypothetical widening of Sebastian Inlet. In this
case the width of the inlet throat section is increased from about 150 m to about 300 meters. The
inlet channel depth is similar to the existing case and ranges from about 3 to 6 m. No major
changes to the interior of the inlet were made to the configuration of the dredged channel
connecting the inlet system to the Intracoastal Waterway to the west.

Figure 19. Configuration of Model Run 7, hypothetical widening of Sebastian Inlet

Figure 20. Predicted tracer concentration for the Model Run 7, wider Sebastian Inlet at day 0 (A), day
150, and day 340 (C).

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Flushing rates and patterns predicted for hypothetical widening of Sebastian Inlet are
similar to those predicted for the existing inlet configuration (Figures 9 and 20). After about 150
days of simulation tracer concentrations remain above 50% percent of the initial value of 20 ppt
over more than half the model domain. More reductions in tracer concentration occur after 340
days of simulation, but similar to the existing case (Model Run 2) tracer values remain well
above 50% the initial 20 ppt over much of the area.

Conclusions
Computed flushing results for existing conditions were similar previous studies, showing
that that the southern portion of the Mosquito Lagoon and the Banana River are poorly flushed at
time scales of several months or more. The Titusville area of the IRL also remained poorly
flushed in model simulations of existing conditions.
The most improved flushing rates and extent resulted from adding either a tidal inlet
inlet or pumping station connection to the coastal ocean across narrow sections of the barrier
island. A narrow tidal inlet or pumping station located in the south compartment of the
Mosquito Lagoon produced complete flushing of the lagoon and north compartment of the IRL
(Grid 1) within 70 days or less. A tidal inlet across the South Cocoa Beach barrier island also
substantially improved flushing of the Banana River included in Grid 2. Opening the water locks
at Port Canaveral also improved flushing but at a somewhat slower rate. This is attributed to the
long conveyance channel between the Port entrance and the Banana River, which may dissipate
tidal energy to a greater degree than a shorter inlet connection. Widening of Sebastian Inlet to
about twice the width at the throat section did not noticeable improve either the rate or extent of
flushing in the IRL

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Wamsley, T., and Zundel, A.K. 2006. Two-dimensional depth-averaged circulation model
CMS-M2D: Version 3, Report 2, Sediment transport and morphology change. ERDC/CHL
TR-06-09, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi.
Demirbilek, Z., and Rosati, J.D. (2011). "Verification and Validation of the Coastal
Modeling System, Report 1: Executive Summary," ERDC/CHL-TR-11-10, US Army
Engineer Research and Development Center, Coastal and Hydraulics Laboratory,
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Army Engineer Research and Development Center, Coastal and Hydraulics Laboratory,
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