1.

INTRODUCTION

This Introduction section provides information relevant to the other sections of this document
and is incorporated by reference into Sections 2 and 3 below.

1.1 Background

NOAAs National Marine Fisheries Service (NMFS) prepared the biological opinion (opinion)
and incidental take statement portions of this document in accordance with section 7(b) of the
Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at
50 CFR 402.

We also completed an essential fish habitat (EFH) consultation on the proposed action, in
accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and
Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600.

We completed pre-dissemination review of this document using standards for utility, integrity,
and objectivity in compliance with applicable guidelines issued under the Data Quality Act
(section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001,
Public Law 106-554). The document will be available through NMFS Public Consultation
Tracking System (https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts). A complete record of
this consultation is on file at NMFS North Central Coast Office in Santa Rosa, California.

1.2 Consultation History

On or about April 17, 2015, the County of San Mateo Department of Public Works (County)
submitted a permit application pursuant to Section 404 of the Clean Water Act to the United
States Army Corps of Engineers (hereafter Corps). On October 13, 2015, NMFS received a
letter dated October 9, 2015, from the Corps requesting initiation of formal consultation for the
Butano Creek Sediment Removal Activities Project in San Mateo County, California (hereafter
referred to as the Project). At that time, the Corps proposed to permit the Project for one year
(work would be performed between June 1 and October 15, 2016). Accompanying the request
was a biological assessment (BA) prepared by H.T. Harvey & Associates (H.T. Harvey &
Associates 2015) for the Corps, including maps and supplemental information.

On December 3, 2015, NMFS received an email from the Corps informing NMFS that the Corps
is authorizing emergency work at the Project site. On December 7 and 8, 2015, NMFS provided
comments and recommendations to the Corps regarding the emergency authorization. No
emergency Project activities occurred, and on December 17, 2015, NMFS received an email
from the Countys consultant (on behalf of the County) informing the regulatory agencies that
due to multiple factors the County elected to not proceed with the (emergency) action at this
time. In that email, the County requested an Individual Permit from the Corps for five years
instead of one year of routine maintenance work at the Project site (Project activities would
commence during the dry season in 2016). On December 22, 2015, NMFS emailed the Corps
requesting clarification from the Corps regarding the permit duration and the number of
maintenance events that may be performed. On April 18, 2016, NMFS received the Corps April

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15, 2016, request for formal consultation on their proposal to issue a five-year Individual Permit.
Included with the request was an updated BA (H.T. Harvey & Associates 2016); formal
consultation was initiated on April 18, 2016. On May 11, 2016, the Corps issued a Public Notice
for the proposed project.

1.3 Proposed Action

Action means all activities or programs of any kind authorized, funded, or carried out, in whole
or in part, by Federal agencies (50 CFR 402.02).

The Corps, under the authority of Section 404 of the Clean Water Act, proposes to authorize the
County to remove up to approximately 1,445 cubic yards of sediment from the Butano Creek
channel beneath the Pescadero Creek Road Bridge, annually for the next five years (2016-2020).
The proposed Project will occur within the Countys right-of-way associated with Pescadero
Creek Road, County-owned property, private property, and agricultural land. Existing sediment
levels beneath the bridge have aggraded approximately 10-12 feet beneath the bridge. The
proposed Project would excavate 2-10 feet of sediment from beneath the bridge and from the
area 30 feet upstream of the bridge and 40 feet downstream of the bridge. Shallower excavations
would occur toward the channel margins and deeper excavation at the center of the channel. The
objective of the Project is to alleviate chronic (low magnitude, frequently occurring) flooding at
Pescadero Creek Road by removing accumulated sediment in the immediate vicinity of the
bridge. The County anticipates that in subsequent years (following the first year of sediment
removal activities) sediment removed will be no more than, and likely less than, 1,455 cubic
yards. The total Project disturbance area is approximately 3.56 acres. Removed sediment will
be disposed at an off-site, upland location. Project activities would occur between June 15 and
October 15. Sediment removal and disposal activities will require approximately two weeks to
complete. The proposed Project also entails the establishment of a Conservation Easement to
provide mitigation for the Projects impacts to California red-legged frog and San Francisco
garter snake habitat. The Project also proposes the creation or restoration of riparian vegetation
at an off-site location.

The proposed Project has been designed with avoidance and minimization measures (Table 2 in
the April 2015 Butano Creek at Pescadero Creek Road Sediment Removal Project: Attachment A
Supplemental Information) that address hazardous materials, spill prevention and control,
equipment maintenance and fueling, etc.).

1.3.1 Staging and Access

Equipment and materials staging will occur on County-owned property near Bean Hollow Road,
approximately 0.3 miles southwest of Pescadero Creek Road Bridge. Staging activities will
occur in heavily disturbed upland areas that are currently used for temporary storage and
parking. Staging may also occur along Pescadero Creek Road within County right-of-way on the
northeast side of the creek crossing. Access to the sediment removal footprint will occur at two
points adjacent to Pescadero Creek Road Bridge: the work area on the north side of the bridge
will be accessed from the northeast side of the bridge, and the work area on the south side of the
bridge will be accessed from the southwest side of the bridge.

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1.3.2 Vegetation Removal

Prior to conducting sediment removal activities, the Project will remove vegetation established
on the accumulated sediment within the creek and access paths to the channel. Thirteen live
trees and one dead tree will be removed. The live trees includes eight alders (6-10 inches in
diameter at breast height [dbh]), one non-native acacia (6-inches dbh), one unidentified 10-inch
dbh tree, and three willows (6-14 inches dbh). Following sediment removal activities each year,
the Project will implement erosion control and best management practices for storm water
management, including limited revegetation such as hydroseeding. Due to the purpose and need
of the Project, most of the removed trees and vegetation, such as trees located below the ordinary
high water mark, will not be replanted within the creek channel. Upon ultimate Project
completion (i.e., after the final years sediment removal), the access routes, cofferdam areas
(described below), and staging areas will be restored.

1.3.3 Fish Relocation and Dewatering

Sediment removal work will be conducted during the summer season when the water level in
Butano Creek is lowest; however, some water is anticipated to be in the channel when annual
sediment removal activities are scheduled to begin. If water is present, then channel dewatering
will occur to allow equipment to access the channel. A cofferdam and pipeline bypass system
will be installed at the southern (upstream) end of the work area to divert flows around the
sediment removal areas. A second cofferdam will be installed at the northern (downstream)
extent of the work area. The pipeline bypass system will route streamflow around the worksite
and return the flow directly back to the creek downstream of the work area. Pumps will be used
to remove any remaining water from between the cofferdams. This dewatering system may be
operated continuously (24 hours per day) until the sediment removal process is complete. Once
sediment is removed, the cofferdams and pipeline will be removed to allow creek flow to return
to the channel in a manner that will allow for the least disturbance to the substrate. Cofferdam
and pipeline installation and removal, and diversion pumping will be implemented and
monitored according to County best management practices (BMPs) and BMP-22 as described in
the April 2015 Butano Creek at Pescadero Creek Road Sediment Removal Project: Attachment A
Supplemental Information.

During cofferdam installation, the downstream cofferdam will be installed first. Most of the
upstream cofferdam, with the exception of an opening large enough for fish passage, will then be
constructed. Then, prior to dewatering, qualified biologists will walk from the downstream
cofferdam upstream while carrying a block net or nets in order to encourage fish to move
upstream and out of the opening in the upstream cofferdam. The block net will then be
positioned to prevent fish from re-entering the dewatering area while the upstream cofferdam is
completed. If insufficient water is present in the area upstream of the Project to support fish, but
sufficient water is present downstream from the Project, then the process will be reversed (with
the upstream cofferdam constructed first, and with fish encouraged to move downstream). After
the biologists place the block nets, the biologists will use electrofishing and/or seining
throughout the sediment removal area to rescue and relocate fish to suitable habitat within
another reach of Butano Creek. The relocation site will be upstream or downstream of the

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sediment removal area, outside of potential disturbance, and will have sufficient water depth,
flow, and cover to allow fish to disperse and/or avoid predation. Electrofishing will be
conducted in accordance with NMFSs Guidelines for Electrofishing Waters Containing
Salmonids Listed under the Endangered Species Act (NMFS 2000).

A qualified biologist will be present during dewatering to relocate all native fish to a suitable
habitat location as needed. All pumps used for dewatering where salmonids may be present will
be screened according to NMFS criteria for juvenile salmonids, and NMFS personnel will be
immediately notified of any observed fish mortality events.

1.3.4 Sediment Removal and Disposal

Most of the sediment adjacent to and under the bridge will be removed through excavation
methods involving use of a telescopic excavator from the top of the bank. Smaller equipment
including a walk-behind mini-track loader (e.g., Bobcat MT-52 or similar) will be used within
the creek channel below the bridge deck where there is not sufficient clearance to use larger
equipment. If necessary due to an abundance of water in the work area, a settling tank and sump
pump will be installed immediately northwest of the bridge to dewater removed sediment
material and to contain suspended soil particles onsite. After sufficient settling, the water will be
discharged from the settling tank to the creek downstream from the Project site, in accordance
with the Countys BMPs (as noted in the April 2015 Butano Creek at Pescadero Creek Road
Sediment Removal Project: Attachment A Supplemental Information.)

Sediment that is removed from Butano Creek will be taken offsite to one of two locations: (1)
private property on Water Lane (the Curry parcel) that is currently used for agricultural practices,
which is the preferred location, or; (2) a nearby County property that is currently used for
storage.

1.3.5 Site Restoration

After sediment removal activities are completed each year, erosion control measures and BMPs
for storm water management will be implemented throughout the disturbed areas, as appropriate.
This may include limited hydroseeding with a native seed mix and installation of erosion control
materials, such as straw, wattles, or sediment fencing. The County has determined they will not
replant trees in, or revegetate the sediment removal area, within Butano Creek because these
areas may be below the ordinary high water mark and/or replanting could impede the restored
flow capacity under Pescadero Creek Road. However, native willow and alder trees surrounding
the sediment removal area are expected to grow rapidly and re-establish in disturbed areas.
Upon completion of the final years sediment removal activities, the Countys contractor will
restore two access routes adjacent to the sediment removal area to pre-Project conditions and
apply hydroseeding with a native seed mix to minimize post-Project erosion.

1.3.6 Annual Maintenance Plan

Sediment removal activities may not be necessary every year for the Project and will never be
performed more than once per year. Each year, County staff will conduct a reconnaissance

4
survey to identify if sediment removal or other vegetation management activities are necessary.
The visual survey will focus on assessing the area upstream (south) and downstream (north) of
the Pescadero Creek Road Bridge crossing at Butano Creek, and include assessing: vegetation
growth and/or accumulation of wood debris; sediment accumulation; potential flood risk; risk to
adjacent infrastructure and agriculture, and; condition of previously replanted areas.

Based on this assessment, the County will prepare a work plan for maintenance activities
proposed to be conducted in that given year. In some years, no maintenance work may be
needed based on site conditions. If stream conveyance capacity is diminished by greater than 30
percent, then sediment removal from the creek is likely necessary. After the first year of
sediment removal work, tree removal to access the work site to remove sediment will be avoided
if feasible. However, if tree removal is needed to access the work area, tree removal will be kept
to a maximum of five trees less than six inches dbh and one tree greater than six inches dbh per
year.

1.3.7 Conservation Easement and Creation/Restoration of Riparian Vegetation

To compensate for temporary impacts to California red-legged frog and San Francisco garter
snake habitat resulting from the Project, habitat on County-owned property southwest of
Pescadero Creek Road and west of Bean Hollow Road will be preserved (via a conservation
easement) and managed (via a Habitat Management and Monitoring Plan) off-site that provides
habitat for these species. In addition, south of the conservation easement a 0.71-acre riparian
restoration area of coastal scrub, jubata grass, and annual grassland will be restored to riparian
wetland habitat to offset a temporary loss of riparian wetland habitats at the sediment removal
site.

1.3.8 Interrelated and Interdependent Activities

Interrelated actions are those that are part of a larger action and depend on the larger action for
their justification. Interdependent actions are those that have no independent utility apart from
the action under consideration (50 CFR 402.02). There are no interrelated or interdependent
activities associated with the proposed Project.

1.4 Action Area

Action area means all areas to be affected directly or indirectly by the Federal action and not
merely the immediate area involved in the action (50 CFR 402.02).

The action area for the Project is located in Butano Creek, near the Town of Pescadero in San
Mateo County and includes the sediment disposal sites, Pescadero Creek Road, and the two
potential staging areas. Within Butano Creek, the action area extends upstream of Pescadero
Creek Road bridge approximately 50 feet and downstream approximately 200 feet of the bridge
where sediment and turbidity may occur during installation and removal of the cofferdams
(between which approximately 180 feet of the creek will be dewatered), where fish may be
released to, and where increased sedimentation and turbidity may occur following the first fall

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rain event following sediment removal activities. The total Project disturbance area is
approximately 3.56 acres.

2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND

INCIDENTAL TAKE STATEMENT

The ESA establishes a national program for conserving threatened and endangered species of
fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a) (2) of
the ESA, Federal agencies must ensure that their actions are not likely to jeopardize the
continued existence of endangered or threatened species, or adversely modify or destroy their
designated critical habitat. Per the requirements of the ESA, Federal action agencies consult
with NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides
an opinion stating how the agencys actions would affect listed species and their critical habitat.
If incidental take is expected, section 7(b)(4) requires NMFS to provide an incidental take
statement (ITS) that specifies the impact of any incidental taking and includes non-discretionary
reasonable and prudent measures and terms and conditions to minimize such impacts.

2.1 Analytical Approach

This biological opinion includes both a jeopardy analysis and an adverse modification analysis.
The jeopardy analysis relies upon the regulatory definition of to jeopardize the continued
existence of a listed species, which is to engage in an action that would be expected, directly or
indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed
species in the wild by reducing the reproduction, numbers, or distribution of that species (50
CFR 402.02). Therefore, the jeopardy analysis considers both survival and recovery of the
species.

This biological opinion relies on the definition of "destruction or adverse modification", which
means a direct or indirect alteration that appreciably diminishes the value of critical habitat for
the conservation of a listed species. Such alterations may include, but are not limited to, those
that alter the physical or biological features essential to the conservation of a species or that
preclude or significantly delay development of such features (81 FR 7214).

We use the following approach to determine whether a proposed action is likely to jeopardize
listed species or destroy or adversely modify critical habitat:

Identify the range wide status of the species and critical habitat likely to be adversely
affected by the proposed action.
Describe the environmental baseline in the action area.
Analyze the effects of the proposed action on both species and their habitat using an
exposure-response-risk approach.
Describe any cumulative effects in the action area.
Integrate and synthesize the above factors to assess the risk that the proposed action poses
to species and critical habitat.
Reach jeopardy and adverse modification conclusions.

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 If necessary, define a reasonable and prudent alternative to the proposed action.

2.2. Range wide Status of the Species and Critical Habitat

This opinion examines the status of each species that would be adversely affected by the
proposed action. The status is determined by the level of extinction risk that the listed species
face, based on parameters considered in documents such as recovery plans, status reviews, and
listing decisions. This informs the description of the species likelihood of both survival and
recovery. The species status section also helps to inform the description of the species current
reproduction, numbers, or distribution as described in 50 CFR 402.02. The opinion also
examines the condition of critical habitat throughout the designated area, evaluates the
conservation value of the various watersheds and coastal and marine environments that make up
the designated area, and discusses the current function of the essential physical and biological
features that help to form that conservation value.

2.2.1 Species Description and General Life History

1. Steelhead

General reviews for steelhead in California document much variation in life history (Shapovalov
and Taft 1954; Barnhart 1986; Busby et al. 1996; McEwan 2001). CCC steelhead are
exclusively winter run fish, typically immigrating from the ocean to freshwater spawning
streams between October and April, with immigration peaking in January and February.
Although variation occurs, in Central Californias coastal streams, rearing juvenile steelhead
usually live in freshwater for 2 years and then migrate to the ocean from January through June,
with peak emigration of smolts to estuaries and the ocean occurring in April and May
(Fukushima and Lesh 1998). After ocean entry they spend 1 or 2 years maturing in the marine
environment before returning to their natal streams to spawn. After spawning, steelhead adults
may return to the ocean and then return to freshwater to spawn up to 4 times over their lifetime.
Thus, unlike other Pacific salmon species, steelhead are iteroparous, or capable of spawning
more than once before death (Busby et al. 1996). However, steelhead rarely spawn more than
twice before dying; most that do so are females (Nickelson et al. 1992). Iteroparity is more
common among southern steelhead populations than northern populations (Busby et al. 1996).
Emergent alevin and steelhead fry rear in edgewater habitats and move gradually into pools and
riffles as they grow larger. Cover is an important habitat component for juvenile steelhead, both
as a velocity refuge and as a means of avoiding predation (Shirvell 1990, Meehan and Bjornn
1991). Peak migration timing of steelhead fry seeking out available habitat within the watershed
occurs in June and early July, although in cool and wet years this distributional migration can
peak in August (Shapavalov and Taft 1954, SEC 1998, Fawcett 2009, Bjorn 1971).

Steelhead juveniles tend to use riffles and other habitats not strongly associated with other cover
types during summer rearing more so than Chinook salmon juveniles. Young steelhead feed on a
wide variety of aquatic and terrestrial insects, and emerging fry are sometimes preyed upon by
older juveniles. Seasonal migrations within watersheds during the freshwater rearing stage of
juvenile steelhead allow individuals to access seasonally productive habitat for opportunities for
rapid growth and to attain minimum threshold sizes for marine survival (Hayes et. al., 2008).

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Rearing steelhead juveniles prefer water temperatures of 7.2-14.4 C and have an upper lethal
limit of 23.9C (Barnhart 1986, Bjornn and Reiser 1991). They can survive short periods in
water up to 27C with saturated dissolved oxygen conditions and a plentiful food supply.
Fluctuating diurnal water temperatures (Busby et al. 1996) and cold groundwater inflows
providing diurnal temperature refuge also aid in survivability of steelhead juveniles in
Mediterranean locales. Juvenile steelhead in streams hold territories close to the substratum
where velocities are lower and sometimes counter to the main stream flow; from these, they can
make forays up into surface currents to take drifting food (Kalleberg 1958). Juveniles rear in
freshwater from one to four years (usually two years), then smolt and migrate to the ocean in
March and April (Barnhart 1986), with a smaller percentage out-migrating in December (Hayes
et al. 2008).

In California DPSs, winter steelhead juveniles usually live in freshwater for two years prior to
smolting (Busby et al. 1996). Steelhead smolts are usually 15-20 centimeters (cm) total length
and migrate to the ocean in the spring (Meehan and Bjornn 1991) or winter (Hayes et al. 2008).
Juvenile steelhead tend to migrate directly offshore during their first summer from whatever
point they enter the ocean rather than migrating along the coastal belt as salmon do (Hartt and
Dell 1986). During the fall and winter, juveniles move southward and eastward (Nickelson et al.
1992).

Steelhead typically reside in marine waters for two or three years prior to returning to their natal
stream to spawn as 4- or 5-year olds. Populations in Oregon and California have higher
frequencies of age-1 ocean steelhead than populations to the north, but age-2 ocean steelhead
generally remain dominant (Busby et al. 1996). Age structure appears to be similar to other west
coast steelhead, dominated by 4-year-old spawners (Busby et al. 1996). Some steelhead return
to fresh water after only two to four months in the ocean or estuaries and are termed half-
pounders (Snyder 1925). Half-pounders generally spend the winter in fresh water and then out
migrate again the following spring for several months before returning to fresh water to spawn.
Half-pounders occur over a relatively small geographic range in southern Oregon and northern
California, and are only reported in the Rogue, Klamath, Mad, and Eel rivers (Snyder 1925,
Barnhart 1986, Kesner and Barnhart 1972, and Everest 1973). In the CCC steelhead DPS, a
small population of steelhead exhibiting an apparent half pounder life history have also been
studied in the Russian River Estuary (Josh Fuller, personal communication, NMFS).

2. Coho salmon

The life history of coho salmon in California has been well documented by Shapovalov and Taft
(1954) and Hassler (1987). In contrast to the life history patterns of other anadromous
salmonids, coho salmon in California generally exhibit a relatively simple three year life cycle.
Adult coho salmon typically begin the freshwater migration from the ocean to their natal streams
after heavy late fall or winter rains breach the sandbars at the mouths of coastal streams
(Sandercock 1991). Delays in river entry of over a month are not unusual (Salo and Bayliff
1958, Eames et al. 1981). Migration continues into March, generally peaking in December and
January, with spawning occurring shortly after arrival to the spawning ground (Shapovalov and
Taft 1954).

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Coho salmon are typically associated with medium to small coastal streams characterized by
heavily forested watersheds; perennially-flowing reaches of cool, high-quality water; dense
riparian canopy; deep pools with abundant overhead cover; instream cover consisting of large,
stable woody debris and undercut banks; and gravel or cobble substrates.

Female coho salmon choose spawning areas usually near the head of a riffle, just below a pool,
where water changes from a laminar to a turbulent flow and small to medium gravel substrate are
present. The flow characteristics surrounding the redd usually ensure good aeration of eggs and
embryos, and flushing of waste products. The water circulation in these areas also facilitates fry
emergence from the gravel. Preferred spawning grounds have: nearby overhead and submerged
cover for holding adults; water depth of 4 to 21 inches; water velocities of 8 to 30 inches per
second; clean, loosely compacted gravel (0.5 to 5 inch diameter) with less than 20 percent fine
silt or sand content; cool water ranging from 39 to 50 degrees Fahrenheit (F) with high
dissolved oxygen of 8 mg/L; and inter-gravel flow sufficient to aerate the eggs. Lack of suitable
gravel often limits successful spawning.

Each female builds a series of redds, moving upstream as she does so, and deposits a few
hundred eggs in each. Fecundity of female coho salmon is directly proportional to size; each
adult female coho salmon may deposit from 1,000 to 7,600 eggs (Sandercock 1991). Briggs
(1953) noted a dominant male accompanies a female during spawning, but one or more
subordinate males may also engage in spawning. Coho salmon may spawn in more than one
redd and with more than one partner (Sandercock 1991). Coho salmon are semelparous meaning
they die after spawning. The female may guard a redd for up to two weeks (Briggs 1953).

The eggs generally hatch after four to eight weeks, depending on water temperature. Survival
and development rates depend on temperature and dissolved oxygen levels within the redd.
According to Baker and Reynolds (1986), under optimum conditions, mortality during this
period can be as low as 10 percent; under adverse conditions of high scouring flows or heavy
siltation, mortality may be close to 100 percent. McMahon (1983) found that egg and fry
survival drops sharply when fine sediment makes up 15 percent or more of the substrate. The
newly-hatched fry remain in the redd from two to seven weeks before emerging from the gravel
(Shapovalov and Taft 1954). Upon emergence, fry seek out shallow water, usually along stream
margins. As they grow, juvenile coho salmon often occupy habitat at the heads of pools, which
generally provide an optimum mix of high food availability and good cover with low swimming
cost (Nielsen 1992). Chapman and Bjornn (1969) determined that larger parr tend to occupy the
head of pools, with smaller parr found further down the pools. As the fish continue to grow, they
move into deeper water and expand their territories until, by July and August; they reside
exclusively in deep pool habitat. Juvenile coho salmon prefer: well shaded pools at least 3.3
feet deep with dense overhead cover, abundant submerged cover (undercut banks, logs, roots,
and other woody debris); water temperatures of 54 to 59 F (Brett 1952, Reiser and Bjornn
1979), but not exceeding 73 to 77 F (Brungs and Jones 1977) for extended time periods;
dissolved oxygen levels of 4 to 9 mg/L; and water velocities of 3.5 to 9.5 inches per second in
pools and 12 to 18 inches per second in riffles. Water temperatures for good survival and growth
of juvenile coho salmon range from 50 to 59 F (Bell 1973, McMahon 1983). Growth is slowed
considerably at 64 F and ceases at 68 F (Stein et al. 1972, Bell 1973).

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Preferred rearing habitat has little or no turbidity and high sustained invertebrate forage
production. Juvenile coho salmon feed primarily on drifting terrestrial insects, much of which
are produced in the riparian canopy, and on aquatic invertebrates growing within the interstices
of the substrate and in leaf litter in pools. As water temperatures decrease in the fall and winter
months, fish stop or reduce feeding due to lack of food or in response to the colder water, and
growth rates slow. During December through February, winter rains result in increased stream
flows. By March, following peak flows, fish resume feeding on insects and crustaceans, and
grow rapidly.

In the spring, as yearlings, juvenile coho salmon undergo a physiological process, or

smoltification, which prepares them for living in the marine environment. They begin to migrate
downstream to the ocean during late March and early April, and out-migration usually peaks in
mid-May, if conditions are favorable. Emigration timing is correlated with peak upwelling
currents along the coast. Entry into the ocean at this time facilitates more growth and, therefore,
greater marine survival (Holtby et al. 1990). At this point, the smolts are about four to five
inches in length. After entering the ocean, the immature salmon initially remain in nearshore
waters close to their parent stream. They gradually move northward, staying over the continental
shelf (Brown et al. 1994). Although they can range widely in the north Pacific, movements of
coho salmon from California are poorly understood.

2.2.2 Status of Species

1. Steelhead

Historically, approximately 70 populations of steelhead existed in the CCC steelhead DPS

(Spence et al. 2008). Many of these populations (about 37) were independent, or potentially
independent, meaning they had a high likelihood of surviving for 100 years absent anthropogenic
impacts (Bjorkstedt et al. 2005). The remaining populations were dependent upon immigration
from nearby CCC steelhead DPS populations to ensure their viability (McElhaney et al. 2000,
Bjorkstedt et al. 2005).

While historical and present data on abundance are limited, CCC steelhead numbers are
substantially reduced from historical levels. A total of 94,000 adult steelhead were estimated to
spawn in the rivers of this DPS in the mid-1960s, including 50,000 fish in the Russian River
the largest population within the DPS (Busby et al. 1996). Near the end of the 20th century,
McEwan (2001) estimated that the wild steelhead population in the Russian River watershed was
between 1,700 and 7,000 fish. Abundance estimates for smaller coastal streams in the DPS
indicate low but stable levels, with recent estimates for several streams (Lagunitas, Waddell,
Scott, San Vicente, Soquel, and Aptos creeks) of individual run sizes of 500 fish or less (62 FR
43937).

Some loss of genetic diversity has been documented and attributed to previous among-basin
transfers of stock and local hatchery production in interior populations in the Russian River
(Bjorkstedt et al. 2005). In San Francisco Bay streams, reduced population sizes and
fragmentation of habitat has likely also led to loss of genetic diversity in these populations. For

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more detailed information on trends in CCC steelhead abundance, see: Busby et al. 1996, NMFS
1997, Good et al. 2005, and Spence et al. 2008

CCC steelhead have experienced serious declines in abundance and long-term population trends
suggest a negative growth rate. This indicates the DPSs may not be viable in the long term. DPS
populations that historically provided enough steelhead immigrants to support dependent
populations may no longer be able to do so, placing dependent populations at increased risk of
extirpation. However, because CCC steelhead have maintained a wide distribution throughout
the DPS, roughly approximating the known historical distribution, CCC steelhead likely possess
a resilience that is likely to slow their decline relative to other salmonid DPSs or ESUs in worse
condition. The 2005 status review concludes that steelhead in the CCC steelhead DPS remain
"likely to become endangered in the foreseeable future" (Good et al. 2005), a conclusion that was
consistent with a previous assessment (Busby et al. 1996) and supported by the most recent
NMFS Technical Recovery Team work (Spence et al. 2008). On January 5, 2006, NMFS issued
a final determination that the CCC steelhead DPS is a threatened species, as previously listed (71
FR 834). Although numbers did not decline further during 2007/08, the 2008/09 adult CCC
steelhead return data indicated a decline in returning adults across their range. Escapement data
from 2009/2010 indicated a slight increase; however, the returns were still well below data
observed within recent decades (Jeffrey Jahn, personal communication, 2010). Based on Warm
Springs Dam Hatchery returns, the steelhead population of the Russian River recovered from the
decadal low of below 1000 fish returning in 2008/09 to 4600 returning in 2012/13, but dropped
to just below 2000 returns in 2013/14 and just above 2000 in the 2014/15 season. Based on
anecdotal reports of sport fishing website chat rooms and personal conversations with sport
fishing enthusiasts and guides (Pers. comm. John McKeon 2015), these return numbers from
Warm Springs Hatchery likely reflect similar abundance trends throughout the wider CCC
steelhead DPS.

The Scott Creek (Santa Cruz county) life cycle monitoring station within the Santa Cruz
Mountains Stratum provides the only population estimates of adult steelhead abundance in the
entire CCC steelhead DPS for a period spanning more than three years. Over the past 12 years,
an average of 202 steelhead adults have returned to this watershed, which is approaching 30
percent of the viability target (Spence 2016). However, the population trend has been negative.
Implementation of the coastal monitoring plan has produced estimates of steelhead in several
other watersheds in this stratum, but only for the past 1-3 years. Results from these surveys
indicate that populations in the three largest watersheds number in the hundreds of fish, from 136
in San Gregorio Creek (San Mateo county) to more than 500 in Pescadero Creek and the San
Lorenzo River (Santa Cruz county). These values range from 7 percent (San Gregorio) to 27
percent (Pescadero Creek) of the viability targets for these populations (Spence 2016).

The 2011 status review by the Williams et al. (2011) concluded that steelhead in the CCC
steelhead DPS remains likely to become endangered in the foreseeable future, and while data
availability for this DPS remains poor, there is little new evidence to suggest that the extinction
risk for this DPS has changed appreciably in either direction since publication of the last viability
assessment (Spence 2016). On December 7, 2011, NMFS affirmed no change to the
determination that the CCC steelhead DPS is a threatened species, as previously listed (NMFS
2011, 76 FR 76386). In April 2016, NMFS issued its 2016 5-Year Review: Summary &

11
Evaluation of Central California Coast Steelhead (NMFS 2016a) and recommended CCC
steelhead DPS remain listed as threatened.

2. Coho salmon

Historically, the CCC coho salmon ESU was comprised of approximately 76 coho salmon
populations. Most of these were dependent populations that needed immigration from other
nearby populations to ensure their long term survival, as described above. Historically, there
were 11 functionally independent populations and one potentially independent population of
CCC coho salmon (Spence et al. 2008, Spence et al. 2012). Most of the populations in the CCC
coho salmon ESU are currently doing poorly; low abundance, range constriction, fragmentation,
and loss of genetic diversity is documented, as described below.

Brown et al. (1994) estimated that annual spawning numbers of coho salmon in California
ranged between 200,000 and 500,000 fish in the 1940s, which declined to about 100,000 fish by
the 1960s, followed by a further decline to about 31,000 fish by 1991. More recent abundance
estimates vary from approximately 600 to 5,500 adults (NMFS 2005). Recent status reviews
(NMFS 2003, NMFS 2005, Williams et al. 2011) indicate that the CCC coho salmon are likely
continuing to decline in number. CCC coho salmon have also experienced acute range
restriction and fragmentation. Adams et al. (1999) found that in the mid 1990s, coho salmon
were present in 51 percent (98 of 191) of the streams where they were historically present, and
documented an additional 23 streams within the CCC coho salmon ESU in which coho salmon
were found for which there were no historical records. Recent genetic research in progress by
both the NMFS Southwest Fisheries Science Center (SWFSC) and the Bodega Marine
Laboratory has documented reduced genetic diversity within CCC coho salmon subpopulations
(Bjorkstedt et al. 2005). The influence of hatchery fish on wild stocks has also contributed to the
poor diversity through outbreeding depression and disease.

Available data from the few remaining independent populations shows continuing declines and
many independent populations that supported the species overall numbers and geographic
distributions have been extirpated. This suggests that populations that historically provided
support to dependent populations via immigration have not been able to provide enough
immigrants for many dependent populations for several decades. The near-term (10 - 20 years)
viability of many of the extant independent CCC coho salmon populations is of serious concern.
These populations may not have enough fish to survive additional natural and human caused
environmental change.

Williams et al. (2011) note that for all available time series, recent population trends have been
downward with particularly poor adult returns from 2006 to 2010. In addition, any independent
populations are well below low-risk abundance targets and several are either extinct or below the
high-risk dispensation thresholds that were identified by Spence et al. (2008). It appears that
none of the five diversity strata defined by Bjorkstedt et al. (2005) currently support viable
populations based on criteria established by Spence et al (2008). The risk of extinction for this
ESU appears to have increased since the last formal review when Good et al. (2005) concluded
that the ESU was in danger of extinction. The best available updated information on the
biological status of this ESU and the threats facing this ESU (Williams et al. 2011, NMFS

12
2011a) indicate that it continues to remain endangered, and its condition is worsening (76 FR
50447). Based on this information, NMFS chose to maintain the endangered listing of CCC
coho salmon. In April 2016, NMFS issued its 2016 5-Year Review: Summary & Evaluation of
Central California Coast Coho Salmon (NMFS 2016b) and determined that no reclassification
for CCC coho salmon ESU is appropriate, and therefore the CCC coho salmon ESU should
remain listed as endangered.

The NMFSs recovery plan (NMFS 2012) for the CCC coho salmon ESU identified the major
threats to population recovery. These major threats include: roads, water diversions and
impoundments; residential and commercial development; and severe weather.

2.2.3 Status of Critical Habitat for CCC steelhead and CCC coho salmon

In designating critical habitat, NMFS considers, among other things, the following requirements
of the species: 1) space for individual and population growth, and for normal behavior; 2) food,
water, air, light, minerals, or other nutritional or physiological requirements; 3) cover or shelter;
4) sites for breeding, reproduction, or rearing offspring; and 5) habitats that are protected from
disturbance or are representative of the historic geographical and ecological distributions of this
species (50 CFR 424.12(b)). The designation of critical habitat uses the term primary constituent
element or essential features. The new critical habitat regulations (81 FR 7414) replace this term
with physical or biological features (PBFs). The shift in terminology does not change the
approach used in conducting a destruction or adverse modification analysis, which is the same
regardless of whether the original designation identified primary constituent elements, physical
or biological features, or essential features. In this biological opinion, NMFS uses the term PBF
to mean primary constituent element or essential feature, as appropriate for the specific critical
habitat.

PBFs for CCC steelhead critical habitat, and their associated essential features within freshwater
include:

1. Freshwater spawning sites with water quantity and quality conditions and substrate
supporting spawning, incubation and larval development;
2. Freshwater rearing sites with:
a. Water quantity and floodplain connectivity to form and maintain physical habitat
conditions and support juvenile growth and mobility;
b. Water quality and forage supporting juvenile development; and
c. Natural cover such as shade, submerged and overhanging large wood, log jams and
beaver dams, aquatic vegetation, large rocks and boulders, side channels, and
undercut banks.
3. Freshwater migration corridors free of obstruction and excessive predation with water
quantity and quality conditions and natural cover such as submerged and overhanging large
wood, aquatic vegetation, large rocks and boulders, side channels, and undercut banks
supporting juvenile and adult mobility and survival.

For CCC coho salmon critical habitat the following PBFs were identified: 1) juvenile summer
and winter rearing areas; 2) juvenile migration corridors; 3) areas for growth and development to

13
adulthood; 4) adult migration corridors; and 5) spawning areas. Within these areas, essential
features of coho salmon critical habitat include adequate: 1) substrate, 2) water quality, 3) water
quantity, 4) water temperature, 5) water velocity, 6) cover/shelter, 7) food, 8) riparian vegetation,
9) space, and 10) safe passage conditions (64 FR 24029).

The condition of CCC steelhead, and CCC coho salmon critical habitat, specifically its ability to
provide for their conservation, has been degraded from conditions known to support viable
salmonid populations. NMFS has determined that currently depressed population conditions are,
in part, the result of the following human-induced factors affecting critical habitat1: logging,
agriculture, mining, urbanization, stream channelization, dams, wetland loss, and water
withdrawals (including unscreened diversions for irrigation). Impacts of concern include altered
stream bank and channel morphology, elevated water temperature, lost quantity or quality of
spawning and rearing habitat, habitat fragmentation, impaired gravel and wood recruitment from
upstream sources, degraded water quality, lost riparian vegetation, and increased erosion into
streams from upland areas (Weitkamp et al. 1995; Busby et al. 1996; 61 FR 56138; 64 FR
24049; 70 FR 37160; 70 FR 52488). Diversion and storage of river and stream flow by seasonal
impoundments, dams and diversions and groundwater pumping has dramatically altered the
natural hydrologic cycle in many of the streams within the DPS and ESU. Altered flow regimes
can delay or preclude migration, dewater aquatic habitat, and strand fish in disconnected pools or
floodplains, while unscreened diversions can entrain juvenile fish.

Due to the cumulative impacts of these conditions across the DPS and ESU, fry emergence rates
have declined, suitable juvenile spring, summer, and winter rearing habitat is limited, and fall
and spring migration windows for both adults and smolts are restricted by flow, temperature, and
sediment transport changes. Where these types of impacts overlap with the potential effects of
the proposed action, we discuss these in more detail in the Environmental Baseline section that
follows.

2.2.4 Global Climate Change

Another factor affecting the range-wide status of the CCC steelhead DPS and the CCC coho
salmon ESU, and aquatic habitat at large is climate change. Impacts from global climate change
are already occurring in California. For example, average annual air temperatures, heat
extremes, and sea level have all increased in California over the last century (Kadir et al. 2013).
Snow melt from the Sierra Nevada has declined (Kadir et al. 2013). However, total annual
precipitation amounts have shown no discernable change (Kadir et al. 2013). Listed salmonids
may have already experienced some detrimental impacts from climate change. NMFS believes
the impacts on listed salmonids to date are likely fairly minor because natural, and local, climate
factors likely still drive most of the climatic conditions steelhead experience, and many of these
factors have much less influence on steelhead abundance and distribution than other human
disturbances across the landscape. In addition, these listed salmonids of the coast range are not
dependent on snowmelt driven streams, and thus not as affected by declining snow packs.

1
Other factors, such as over fishing and artificial propagation, have also contributed to the current population status
of these species. All these human induced factors have exacerbated the adverse effects of natural environmental
variability from such factors as drought and poor ocean conditions.

14
The threat to CCC steelhead and CCC coho salmon from global climate change will increase in
the future. Modeling of climate change impacts in California suggests that average summer air
temperatures are expected to continue to increase (Lindley et al. 2007; Moser et al. 2012). Heat
waves are expected to occur more often, and heat wave temperatures are likely to be higher
(Hayhoe et al. 2004, Moser et al. 2012; Kadir et al. 2013). Total precipitation in California may
decline; critically dry years may increase (Lindley et al. 2007; Schneider 2007; Moser et al.
2012). Wildfires are expected to increase in frequency and magnitude (Westerling et al. 2011,
Moser et al. 2012).

In the San Francisco Bay region, warm temperatures generally occur in July and August, but as
climate change takes hold, the occurrences of these events will likely begin in June and could
continue to occur in September (Cayan et al. 2012). Climate simulation models project that the
San Francisco region will maintain its Mediterranean climate regime, but experience a higher
degree of variability of annual precipitation during the next 50 years that are drier than the
historical annual average during the middle and end of the twenty-first century. The greatest
reduction in precipitation is projected to occur in March and April, with the core winter months
remaining relatively unchanged (Cayan et al. 2012).

Estuaries may also experience other changes detrimental to salmonids. Estuarine productivity is
likely to change based on changes in freshwater flows, nutrient cycling, and sediment amounts
(Scavia et al. 2002, Ruggiero et al. 2010). In marine environments, ecosystems and habitats
important to juvenile and adult salmonids are likely to experience changes in temperatures,
circulation, water chemistry, and food supplies (Brewer and Barry 2008, Feely 2004, Osgood
2008, Turley 2008, Abdul-Aziz et al. 2011, Doney et al. 2012). The projections described above
are for the mid to late 21st Century. In shorter time frames, climate conditions not caused by the
human addition of carbon dioxide to the atmosphere are more likely to predominate (Cox and
Stephenson 2007, Santer et al. 2011).

2.3 Environmental Baseline

The environmental baseline includes the past and present impacts of all Federal, state, or
private actions and other human activities in the action area, the anticipated impacts of all
proposed Federal projects in the action area that have already undergone formal or early section
7 consultation, and the impact of state or private actions which are contemporaneous with the
consultation in process (50 CFR 402.02).

2.3.1 Location and General Habitat Description

The project area is located approximately 0.7 miles west of the Town of Pescadero. Butano
Creek is the largest tributary to Pescadero Creek and the confluence is located in the Pescadero
Marsh Natural Preserve. The Pescadero Road Bridge is located near the base of the Butano
Creek watershed at the upstream extent of the Pescadero Marsh Natural Preserve. Pescadero
Marsh drains into the Pacific Ocean. The Butano Creek watershed drains approximately 21
square miles.

15
Butano Creek within and near the Action Area supports a densely vegetated riparian wetland.
Dominant vegetation in the riparian wetland habitat includes large stands of arroyo willow (Salix
lasiolepis), white alder (Alnus rhombifolia), and American dogwood (Cornus sericea ssp.
occidentalis), with an understory of pacific silverweed (Potentilla anserine ssp. pacifica) and
bulrush (Scirpus microcarpus). Habitat within the sediment removal footprint and associated
equipment access areas is generally composed of this wooded riparian wetland. The Butano
Creek channel within the sediment removal area is approximately 50 feet wide and provides
aquatic habitat with relatively shallow water depths of less than two feet. Due to its sandy and
silty substrate, steelhead are not expected to spawn in the Action Area, but may rear there, and
do migrate through the Action Area. The existing accumulation of sediment in the channel under
the Pescadero Creek Road Bridge may be impairing fish passage because the reduction in
vertical clearance underneath the bridge (NMFS 2010).

South of the bridge and upstream of the sediment removal area, the riparian wetland continues
with emergent seasonal wetlands at the margins along Bean Hollow Road on the west and the
adjacent agricultural field on the east. Downstream of the sediment removal area, Butano Creek
flows into a network of shallow, braided channels that lack a well-defined stream course and
supports wooded riparian wetland and perennial marsh. Butano Creek in the Action Area is
typically wet and flowing, except during drought years when this reach of the channel may be
dry (as it was in the summer of 2015). Upstream water diversions likely have some impact on
streamflow in the action area, though this has not been quantified.

Approximately one mile upstream of the action area, the Butano Creek Floodplain Restoration
Project - which is expected to improve salmonid habitat and promote sediment deposition (cbec
2014) will be implemented upstream during the summer of 2016. The project is designed to
allow for greater hydrologic connectivity with respect to inundation frequency within the
floodplain. The project includes restoration actions at five sites along Butano Creek and involve
construction of engineered log jams, floodplain connector channels, and recruitment of living
bank-side alder trees (Corps 2016).

2.3.2 Fish Abundance

1. Steelhead

Historic estimates of the adult population size in Butano Creek do not exist and only a few
estimates are available for the entire Pescadero Creek watershed. Based on these estimates,
recent observations, and the known impairments throughout the Pescadero and Butano Creek
watersheds, the Pescadero Creek steelhead population has declined significantly over the past
100 years.

Pescadero Creek was one of four A-1 streams noted in San Mateo County in a 1912 California
Department of Fish and Game (CDFG) letter and appears to have supported the largest steelhead
run in the county historically (Becker et al. 2010). In a 1967 report, the annual steelhead run of
Pescadero Creek was estimated to consist of 1,500 spawning adults (Becker et al. 2010). The
system undoubtedly supported many more steelhead (and coho salmon) before any major
degradation of the stream drainage began. For example, in 1870 a commercial fishery existed

16
where a wagon load of steelhead and coho salmon, each weighing 1-14 kilograms, was taken
daily from Pescadero Creek between October and March (Titus et al. 2010). It is reasonable to
assume that the anadromous fish populations were previously larger than the 1967 estimate as
evidenced by the presence of the commercial fishery in 1870 (Titus et al. 2010).

In spring 2013, an outmigrant fyke trap was installed on Pescadero Creek, at approximately river
mile 1.8. In 41 days of trapping between March 25 and May 31, 83 adult steelhead were
collected (CEMAR 2013). While these 83 adults do not constitute a complete annual run for
Pescadero Creek, as many adults likely emigrated after spawning before the trap was installed, it
does highlight that current abundance estimates for the Pescadero Creek watershed are
significantly lower than historical estimates.

The action area is located within a reach of Butano Creek that is migration and rearing habitat for
CCC steelhead. Although there are no known juvenile steelhead density estimates for the action
area, the California Department of Fish and Wildlife (CDFW) conducted juvenile surveys in the
Butano Creek headwaters in October 2013 (CDFW 2014). Three reaches were electrofished
with the following steelhead-per-mile estimates: 515, 718, and 1,311 (or, in fish-per-foot: 0.10,
0.14, and 0.25). As CDFW noted, even though the population estimate calculated at each
station is crude and is an underestimate, owing to limited second-pass capture efficiency, the
resulting calculations of steelhead per mile are relatively consistent in their order of magnitude
and among adjacent sites. The extrapolated results also compare well to the results of single-
pass sampling conducted in 2012 by CDFW, and from 1995 CDFW surveys in other regional
streams of similar habitat size (CDFW 2014). Because we do not have project reach-specific
juvenile steelhead density estimates, we have used CDFWs upper Butano Creek estimates as a
proxy for the project reach; the highest fish-per-foot estimate was 0.25. We also did not know
the current status of the steelhead run when these surveys occurred, nor weather/habitat
conditions. NMFS expects there is likely to be interannual variation in steelhead abundance
during the next five years, resulting in high steelhead abundance in some years, and for this
biological opinion we are using the highest density estimate and increasing it modestly to allow
for annual variation. Thus, based on 0.25 fish per foot, 180 feet proposed to dewatered, and a
modest increase of five fish, NMFS anticipates no more than 50 juvenile steelhead (0.25 x 180 +
5) will be found within the portion of the action area dewatered during dewatering and fish
relocation activities.

2. Coho salmon

Coho salmon in the Pescadero Creek watershed are nearly extirpated (NMFS 2012). During the
2014-2105 spawning season, three coho salmon carcasses were recovered in Pescadero Creek
all three were from hatchery releases into Scott Creek (in Santa Cruz county) and were coded-
wire tagged (B. Spence, pers. comm.). In the summer of 2015, snorkel surveys were conducted
in the mainstem Pescadero Creek, as well as a tributary, but were unable to confirm successful
reproduction. Given that adult returns to Scott Creek were extremely low in 2015-2016
compared to 2014-2015 despite the release of nearly 30,000 smolts in 2014, the likelihood of
appreciable numbers of adult coho that may have returned to the Pescadero Creek watershed is
very low (B. Spence, pers. comm).

17
Given that (1): the proposed action will occur for the next five years; (2) the proposed action
may improve fish passage conditions; and (3) the Butano Creek Floodplain Restoration Project -
which is expected to improve salmonid habitat will be implemented upstream during the
summer of 2016, it is reasonably likely that coho salmon will return to the Pescadero Creek
watershed in the next five years. However, since there have only been sparse reports of coho
salmon in the Pescadero Creek watershed during the last two decades, NMFS expects the
likelihood of juvenile coho salmon being present in the small action area during the next five
years to be low. Based on the expected low number of adult returns, the number of juvenile coho
rearing in the action area during summer season sediment removal events is anticipated to be no
more than five juvenile coho salmon per year.

2.3.4 Previous Section 7 Consultations in the Action Area

Pursuant to section 7 of the ESA, NMFS has completed two interagency consultations that may
have affected the action area of this project.

In 2012, NMFS and the NOAA Restoration Center completed a consultation for the mechanical
breaching of the Pescadero lagoon sandbar. The purpose of this project was to prevent poor
water quality conditions from developing in the lagoon to such a level that a fish kill is likely by
conducting a pre-emptive breach to lower lagoon head pressure and minimize the amount of time
a portion of the marsh is flooded. NMFS concurred with the NOAA Restoration Center that the
project was not likely to adversely affect CCC steelhead or adversely affect its designated critical
habitat, nor that of CCC coho salmon. A mechanical breach occurred in October 2012. Water
surface elevation in Butano Creek at the sediment removal site may have been slightly decreased
as a result of the mechanical breach.

In October 2015, NMFS and the NOAA Restoration Center again completed consultation for
additional breaching proposed to occur in 2015 and 2016; no mechanical breaches occurred in
2015.

NMFS has issued section 10(a)(1)(A) research and enhancement permits and section 4(d) limits
or exceptions for scientific research and monitoring that could potentially occur in the Butano
Creek watershed and the action area. Salmonid monitoring approved under these programs
includes carcass surveys, smolt outmigration trapping, and juvenile density surveys. In general,
these activities are closely monitored and require measures to minimize take during the research
activities.

2.4 Effects of the Action

Under the ESA, effects of the action means the direct and indirect effects of an action on the
species or critical habitat, together with the effects of other activities that are interrelated or
interdependent with that action, that will be added to the environmental baseline (50 CFR
402.02). Indirect effects are those that are caused by the proposed action and are later in time,
but still are reasonably certain to occur.

18
The proposed Project has been designed with avoidance and minimization measures (Table 2 in
the April 2015 Butano Creek at Pescadero Creek Road Sediment Removal Project: Attachment A
Supplemental Information) that address hazardous materials, spill prevention and control,
equipment maintenance and fueling, etc. NMFS has reviewed these measures and, based on our
experience with similar projects and measures, expects these measures will be effective in
avoiding adverse effects to listed salmonids and designated critical habitat.

2.4.1 Fish Relocation Activities

To facilitate annual sediment removal activities, the project proposes to dewater approximately
180 feet of Butano Creek each year, which will necessitate fish capture and relocation prior to
dewatering to avoid fish stranding and exposure to sediment removal activities. Relocation
activities will occur during the summer low-flow period after emigrating smolts (steelhead and
coho) and kelts (post-spawned steelhead adults) have left the creek. Therefore, NMFS expects
only capture of the juvenile lifestage (pre-smolt) steelhead and coho salmon. Before and during
dewatering of the project site, juvenile steelhead, coho salmon, and other fish will be captured by
seining, dip netting, and/or backpack electrofishing. Collected fish will be relocated either
upstream or downstream of the project site. Final location will depend on the quality of habitat
available during actual implementation and this determination will be made by the qualified
biologist conducting the work.

Data to precisely quantify the amount of steelhead and coho salmon that would be present within
the action area prior to relocation activities are not available and vary annually. As described
above, NMFS anticipates no more than 50 juvenile steelhead will be present within the action
area prior to relocation and dewatering activities. Based on the best available information,
NMFS anticipates no more than 5 juvenile coho salmon may be present within the action are
prior to relocation and dewatering activities.

Fish relocation activities pose a risk of injury or mortality to juvenile salmonids. Any fish
collecting gear, whether passive (Hubert 1983) or active (Hayes 1983) has some associated risk
to fish, including stress, disease transmission, injury, or death. The amount of unintentional
injury and mortality attributable to fish capture varies widely, depending on the methods used,
the ambient conditions, and expertise of the field crew. Since fish relocation activities will be
conducted by qualified fisheries biologists, direct effects to, and mortality of juvenile salmonids
during capture will be minimized.

Although sites selected for relocating fish should have similar water temperature as the capture
sites and are expected to have adequate habitat available, in some instances relocated fish may
endure short-term stress from crowding at the relocation sites. Relocated fish may have to
contend with other fish causing increased competition for available resources such as food and
habitat area. Frequent responses to crowding by steelhead include emigration and reduced
growth rates (Keeley 2003). Some the fish released at the relocation sites may choose not to
remain in these areas and move either upstream or downstream to areas that have more vacant
habitat and a lower density of steelhead. As each fish moves, competition remains either
localized to a small area or quickly diminishes as fish disperse. NMFS does not expect impacts
from increased competition will be large enough to adversely affect the survival chances of

19
individual steelhead or coho salmon, or cascade through the watershed population based on the
small area that will likely be affected and the relatively small numbers of individuals likely to be
relocated (particularly when compared with the remainder of individuals throughout the drainage
not affected by this project). Sufficient habitat appears to be available in Butano Creek to sustain
fish relocated without crowding of other juvenile steelhead and coho salmon.

Based on information from other relocation efforts, NMFS estimates injury and mortalities will
be less than three percent of those steelhead and coho salmon that are relocated. Data on fish
relocation efforts since 2004 shows most mortality rates are below three percent for steelhead
(Collind 2004, CDF 2005, 2006, 2007, 2008, 2009, 2010a, 2010b). Fish that avoid capture
during relocation efforts may be exposed to risks described in the following section on
dewatering.

2.4.2 Dewatering

The project proposes to isolate the work area with cofferdams and bypass streamflow around the
sediment removal area. Dewatering of the channel will affect approximately 180 feet of Butano
Creek for approximately two weeks. NMFS anticipates temporary changes to instream flow
within and downstream of the project site during the dewatering process. These fluctuations in
flow are anticipated to be small, gradual, and short-term. Once the cofferdams and pipeline
bypass are installed and operations, stream flow above and below the work site should be the
same as the pre-project conditions except within the dewatered work area where streamflow is
bypassed. The dewatering of approximately 180 of channel is expected to cause a temporary
reduction of aquatic habitat. Juvenile steelhead and coho salmon that avoid capture in the work
area following relocation efforts may die due to desiccation, thermal stress, or by being crushed
by equipment or foot traffic if not found by biologists while water levels within the reach recede.
However, due to the pre-dewatering fish relocation efforts, NMFS expects the number of
juvenile steelhead and coho salmon that will be killed as a result of stranding during dewatering
activities will be less than one percent of the fish within the action area prior to dewatering.

The temporary cofferdams and water diversion structures in the creek are not expected to impact
juvenile steelhead and coho salmon movements in Butano Creek beyond typical summer low-
flow conditions. Although steelhead and coho salmon may not experience intermittent
conditions in the action area during most summers (portions of the work area was dry in Summer
2015), the limited duration of water diversion (approximately two weeks) is unlikely to adversely
affect individual salmonids rearing upstream or downstream of the dewatered reach.

Benthic (i.e., bottom dwelling) aquatic macroinvertebrates (a salmonid prey item) within the
project site may be killed or their abundance reduced when creek habitat is dewatered (Cushman
1985). However, effects to aquatic macroinvertebrates resulting from streamflow diversions and
dewatering will be temporary because project activities will be relatively short-lived and the
dewatered reach is small. Rapid recolonization (typically one to two months) of disturbed areas
by macroinvertebrates is expected following channel rewatering (Cushman 1985, Thomas 1985,
Harvey 1986). In addition, the effect of macroinvertebrate loss on juvenile salmonids is likely to
be negligible because food from upstream sources (via drift) would be available via transport
from the bypass pipeline and immediately downstream of the site. Food sources derived from

20
the riparian zone would not be affected by the project. Based on the foregoing, NMFS does not
expect the loss of macroinvertebrates as a result of dewatering activities will adversely affect
CCC steelhead or CCC coho salmon during this short period.

As described above, NMFS expects annual injury and mortality of juvenile steelhead and coho
salmon associated with relocation to be less than three percent of the total amount of salmonids
captured, and annual mortality associated with dewatering activities to be less than one percent
of the number of salmonids present within the action area prior to dewatering. Given the
relatively low numbers of salmonids expected in the project reach, our assumption of three
percent injury or mortality for relocation activities, and less than one percent mortality for
dewatering activities, NMFS expects no more than three juvenile salmonids (0.04 x 55) will be
injured or killed by fish relocation or dewatering activities.

2.4.3 Sedimentation and Turbidity

The proposed action will result in the disturbance of the creek bed and banks during sediment
removal activities, equipment access, and the construction and removal of the cofferdams.
Disturbed soils may become mobilized when fall and winter storms increase streamflow levels
post-Project activities. Each year when the activities occur, NMFS anticipates these activities
will result in small-short term increases in turbidity during rewatering and subsequent higher
flows during winter storms. Instream and near-stream construction activities have been shown to
result in temporary increases in turbidity (reviewed in Furniss et al. 1991, Reeves et al. 1991,
Spence et al. 1996).

Sediment may affect fish in a variety of ways. High concentrations of suspended sediment can
disrupt normal feeding behavior and efficiency (Cordon and Kelley 1961, Bjornn et al. 1977,
Berg and Northcote 1985), reduced growth rates (Crouse et al. 1981), and increase plasma
cortisol levels (Servizi and Martens 1992). High and prolonged turbidity concentrations can
reduce dissolved oxygen in the water column, result in reduced respiratory functions, reduce
tolerance to diseases, and can also cause fish mortality (Sigler et al. 1984, Berg and Northcote
1985, Gregory and Northcote 1993, Velagic 1993, Waters 1995). Even small pulses of turbid
water can cause salmonids to disperse from established territories (Waters 1995), which can
displace fish into less suitable habitat and/or increase competition and predation, decreasing
chances of survival. Increased sediment deposition can fill pools thereby reducing the amount of
potential cover and habitat available, and smother coarse substrate particles which can impair
macroinvertebrate composition and abundance (Sigler et al. 1984, Alexander and Hansen 1986).

Although sediment and turbidity may affect steelhead and coho salmon as described above,
sedimentation and turbidity levels associated with this project during cofferdam construction and
removal, sediment removal activities, and subsequent rewetting of the project area, are not
expected to rise to the levels discussed in the previous paragraph as described below.

NMFS anticipates any resulting elevated turbidity levels would be small and only occur for a
short time, well below levels and durations shown in the scientific literature as causing injury or
harm to salmonids (see for example Sigler et al. 1984 or Newcombe and Jensen 1996). NMFS
expects any sediment or turbidity generated by the project would not extend more than 200 feet

21
downstream of the work site based on the site conditions (low flows) and methods used to
control sediment and turbidity (isolation of the work space from streamflows, silt fences, etc.).
NMFS does not anticipate adverse effects (e.g., harm, injury, or behavioral impacts) to CCC
steelhead and coho salmon associated with exposure to elevated suspended sediment levels that
would be generated by this project.

2.4.4 Vegetation removal

Prior to conducting sediment removal activities, the Project will annually remove vegetation
established on the accumulated sediment within the creek and access paths to the channel.
Thirteen live trees and one dead tree will be removed during the first annual sediment removal
event. For subsequent annual sediment removal events over the five-year permit term, if tree
removal is needed to access the work area, tree removal will be kept to a maximum of five trees
less than six inches dbh and one tree greater than six inches dbh per year. The applicant will
conduct limited revegetation such as hydroseeding, but most of the removed trees and
vegetation, such as trees located below the ordinary high water mark, will not be replanted
within the creek channel.

Vegetation removal can affect stream-dwelling salmonids by increasing sun exposure and
increasing water temperature, depressing allochthanous food input, and cause erosion of newly
exposed soil. However, the low number of trees removed during the Project is unlikely to have
much impact on stream temperature or food input, considering the densely vegetated and wooded
riparian wetland within, upstream, and downstream of the Project site. Soil erosion will be
minimized by hydroseeding and appropriate sediment controls methods (i.e., fiber rolls, silt
fences [Table 2 in the April 2015 Butano Creek at Pescadero Creek Road Sediment Removal
Project: Attachment A Supplemental Information]). Additionally, native willow and alder trees
surrounding the sediment removal area are expected to grow rapidly and re-establish in disturbed
areas. Thus, NMFS anticipates the temporary loss of vegetation will result in undetectable
effects on stream temperature, food input, and erosion.

2.4.5 Sediment removal

Based on Solutions to Flooding on Pescadero Creek Road (cbec 2014), immediately after
sediment is removed, water levels would be reduced during a 2-year flow event; however, the
road would still flood during this size of event. The frequency and duration of chronic flooding
would be reduced, at least initially until sediment fills in the dredged area. While the frequent
flooding of Pescadero Creek Road at the bridge would be reduced, adjacent floodplain areas to
the north and south of the road would still flood, although to a lesser extent. During a 10-year
flood event, flooding of the road would still occur as the flow rate occurring during the peak of
the flood would exceed the amount that could be conveyed through the dredged bridge opening.

The volume of sediment removed to create this capacity is small relative to the average amount
of sediment currently being transported to Pescadero Marsh Natural Preserve. Results of
sediment transport simulation covering 10 years of historical flow indicate that after the first
significant flood event (e.g., a 2-year or larger event), the channel at the bridge will have filled in
to almost the pre-dredged capacity (cbec 2016). Nonetheless, NMFS expects the Project may

22
have short-term benefits to fish passage by temporarily increasing the channel capacity following
sediment removal activities.

Due to its sandy and silty substrate, the Action Area is not expected to provide spawning habitat
for listed anadromous salmonids and spawning is unlikely to occur downstream of the action
area. Thus, the removal of sediment is not expected to result in the degradation of spawning
habitat. However, juvenile steelhead and coho salmon are likely to reside in the action area and
removing sediment may result in the direct removal of prey resources. As described above,
NMFS does not expect the loss of macroinvertebrates as a result of dewatering activities will
adversely affect CCC steelhead or coho salmon during this short period. Based on the same
rationalization (i.e., rapid recolonization by macroinvertebrates, food available via drift) and
because after the first significant flood event the channel at the bridge is expected to fill in to
almost the pre-dredged capacity, NMFS does not expect the loss of macroinvertebrates as a
result of removing sediment will adversely affect listed salmonids during this period.

2.4.6 Toxic Chemicals

Sediment removal activities in Butano Creek will involve the use of heavy machinery in the
dewatered channel bed. The use of heavy machinery in creek channels creates the potential for
toxic materials associated with mechanical equipment, such as fuels, motor oils, and antifreeze to
enter the stream or channel. Oils and similar substances from construction equipment can
contain a wide variety of polynuclear aromatic hydrocarbons (PAHs), and metals. Both can
result in adverse impacts to salmonids. PAHs can alter salmonid egg hatching rates and reduce
egg survival as well as harm the benthic organisms that are a salmonid food source (Eisler 2000).
Some of the effects that metals can have on salmonids are: immobilization and impaired
locomotion, reduced growth, reduced reproduction, genetic damage, tumors and lesions,
developmental abnormalities, behavior changes (avoidance), and impairment of olfactory and
brain functions (Eisler 2000).

The project has included several measures which reduce the chances of toxins entering streams.
These measures ensure that instream construction work only occurs during the dry season (June
15 - October 15). The County and its contractors propose to maintain any and all fuel storage
and refueling site in an upland location well away from the stream channel; that vehicles and
construction equipment be in good working condition, showing no signs of fuel or oil leaks, and
that any and all servicing of equipment be conducted in an upland location. For instream
activities, NMFS does not anticipate any localized or appreciable water quality degradation from
toxic chemicals or adverse effects to ESA-listed salmonids associated with the proposed project,
as the stream will be dewatered, giving the County and its contractors ample opportunity to
attend to any spill prior to toxic chemicals reaching the waters of Butano Creek. NMFS
anticipates that proposed BMPs and responses by the applicant to any accidental spill of toxic
materials should be sufficient to restrict the effects to the immediate area and not enter the
waterway. Due to these measures, NMFS expects that accidents will be minimized and toxic
chemical contamination of the action area will be minimized to levels which are not likely to
adversely affect listed salmonids or designated critical habitat.

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2.4.7 Critical Habitat Effects Summary

Butano Creek is designated critical habitat for CCC steelhead and CCC coho salmon. Generally
speaking, elements of critical habitat for steelhead and coho salmon found within the action area
include sites for migration and rearing2; coho salmon and steelhead critical habitat within the
action area likely provides juvenile summer and wintering areas; juvenile migration corridors;
and areas for growth and development to adulthood. Potential impacts to designated critical
habitat arising from the proposed action included degraded water quality (i.e., elevated turbidity)
and temporary loss habitat space and prey resources. Based on the relatively small size of the
action area (approximately 180 feet of dewatering and approximately 100 feet of sediment
removal [upstream and downstream lengths, plus beneath the bridge]) and relatively short
duration of project activities (approximately 2 weeks), NMFS expects that any adverse effects
that occur during the five-year permit period will be minor and temporary and not impair the
conditions that support conservation of the species in the action area.

2.4.8 Conservation Easement and Creation/Restoration of Riparian Vegetation

To compensate for temporary impacts to California red-legged frog and San Francisco garter
snake habitat resulting from the Project, habitat on County-owned property southwest of
Pescadero Creek Road and west of Bean Hollow Road will be preserved (via a conservation
easement) and managed (via a Habitat Management and Monitoring Plan) off-site that provides
habitat for these species. This habitat preservation is expected to have no effect on listed
salmonids or their designated critical habitat. In addition, south of the conservation easement a
0.71-acre riparian restoration area of coastal scrub, jubata grass, and annual grassland will be
restored to riparian wetland habitat to offset a temporary loss of riparian wetland habitats at the
sediment removal site.

The planned riparian restoration is expected to improve the restoration sites wildlife habitat
value by removing non-native, invasive plant species that provide little habitat value to wildlife
and by re-establishing native mid- and upper-canopy species. Although not clearly quantifiable
for salmonid habitat, NMFS expects some indirect benefits (i.e., improving native plant
communities at the watershed level will be an improvement over existing conditions and
sediment delivery is expected to decrease).

2.5 Cumulative Effects

Cumulative effects are those effects of future state or private activities, not involving Federal
activities, that are reasonably certain to occur within the action area of the Federal action subject
to consultation (50 CFR 402.02). Future Federal actions that are unrelated to the proposed action
are not considered in this section because they require separate consultation pursuant to section 7
of the ESA. Diversion and storage of stream flow upstream of the action area is likely to
continue into the future, potentially impacting fish and designated critical habitat within the
action area. Altered flow regimes can delay or preclude migration, dewater aquatic habitat, and
strand fish in disconnected pools or floodplains, while unscreened diversions can entrain juvenile

2
See Section 2.2.3 Status of Critical Habitat above for a detailed listing of steelhead and coho salmon PBFs.

24
fish. In the long term, climate change may produce temperature, precipitation, and other changes
that may adversely affect steelhead and coho salmon habitat in the action area.

2.6 Integration and Synthesis

The Integration and Synthesis section is the final step in our assessment of the risk posed to
species and critical habitat as a result of implementing the proposed action. In this section, we
add the effects of the action (Section 2.4) to the environmental baseline (Section 2.3) and the
cumulative effects (Section 2.5), taking into account the status of the species and critical habitat
(Section 2.2), to formulate the agencys biological opinion as to whether the proposed action is
likely to: (1) reduce appreciably the likelihood of both the survival and recovery of a listed
species in the wild by reducing its numbers, reproduction, or distribution; or (2) reduce the value
of designated or proposed critical habitat for the conservation of the species.

CCC steelhead are listed as threatened. Historic estimates of the adult population size in Butano
Creek do not exist and only a few estimates are available for the entire Pescadero Creek
watershed. Based on these estimates, recent observations, and the known impairments
throughout the Pescadero and Butano Creek watersheds, the Pescadero Creek steelhead
population has declined significantly.

CCC coho salmon are listed as endangered. Coho salmon in the Pescadero Creek watershed are
nearly extirpated and only three hatchery adults may have spawned here in recent years. The
likelihood of juvenile coho salmon occurring in the action area during project activities within
the next five years is low. Although adult returns of coho salmon are expected to be low, some
juvenile coho may rear within the action area of Butano Creek within the five-year term of this
Corps permit.

The project is scheduled to be implemented annually for the next five years. The project
proposes to dewater a relatively small reach of Butano Creek (180 feet), and, therefore, the
number of individual salmonids present is anticipated to be relatively small (no more than 50
juvenile steelhead and no more than 5 juvenile coho salmon each year). Due to the timing of
project activities, no adults or smolt would be affected by the project.

As described in the Effects of the Action section above, NMFS identified dewatering and fish
relocation as the adverse effects on CCC steelhead and CCC coho salmon in the action area that
would result from the proposed project. Prior to dewatering the site, fish would be collected and
relocated from the work area. Fish that elude capture and remain in the project area during
dewatering may die due to dessication or thermal stress, or be crushed if not found by biologists
or relocation efforts. However, based on the low mortality rates for similar capture and
relocation efforts, NMFS anticipates few juvenile salmonids would be injured or killed by fish
relocation and sediment removal activities during implementation of the project. Anticipated
mortality from capture and relocation is expected to be less than three percent of the total number
of fish relocated, and mortality expected from dewatering is expected to be less than one percent
of the fish in the action area prior to dewatering. Because no more than 55 juvenile salmonids
are expected to be present each year, NMFS expects no more than 3 juvenile salmonids would be
injured or killed each year by fish relocation and dewatering. Due to the relatively large number

25
of juveniles produced by each spawning pair, steelhead spawning in Butano Creek and the
Pescadero Creek watershed in future years are expected to produce enough juveniles to replace
the few that may be lost at the project site due to relocation and dewatering. It is unlikely that
the small potential loss of juveniles by this project will impact future adult returns. Because
coho salmon numbers are expected to be very low in Butano Creek, juvenile coho presence in
the action area is likely to be low and the majority of coho in the watershed are anticipated to be
upstream where habitat conditions are better and would be preferred by coho salmon. Thus,
even though the overall number of coho salmon in the watershed is low, NMFS expects the coho
salmon juveniles upstream have better chances of contributing to future coho returns to the
watershed than the individuals that would be rearing within the action area.

Dewatering 180 feet of the creek channel for approximately two weeks will result in temporary
and minor adverse effects to a small section of designated critical habitat. However, the project
may temporarily improve fish passage for a short time each year. Sediment and vegetation
removal are also expected to result in temporary and minor adverse effects to a small section of
designated critical habitat. These impacts only occur for two weeks each year and after this time
period, critical habitat is expected to return to its previous condition with no lasting impact on its
value for species conservation, including no impact on the processes and functions that support
species conservation.

Regarding future climate change effects in the action area, California could be subject to higher
average summer air temperatures and lower total precipitation levels. Higher air temperatures
would likely warm stream temperatures. Reductions in the amount of precipitation would reduce
stream flow levels in Central Coast streams. Estuaries may also experience changes in
productivity due to changes in freshwater flows, nutrient cycling, and sediment amounts. For
this project, construction activities would occur for five years and effects are temporary and
minor. As noted above, habitat is expected to return to its previous condition. Effects of climate
change noted above are unlikely to be discernable within that time frame.

2.7 Conclusion

After reviewing and analyzing the current status of critical habitat, the environmental baseline
within the action area, the effects of the proposed action, any effects of interrelated and
interdependent activities, and cumulative effects, it is NMFS biological opinion that the County
of San Mateo, Department of Public Works proposal to remove sediment from Butano Creek,
and to be permitted by the Corps, is not likely to destroy or adversely modify critical habitat
designated for CCC steelhead or CCC coho salmon.

After reviewing and analyzing the current status of the listed species, the environmental baseline
within the action area, the effects of the proposed action, any effects of interrelated and
interdependent activities, and cumulative effects, it is NMFS biological opinion that the
proposed action is not likely to jeopardize the continued existence of CCC steelhead or CCC
coho salmon.

26
2.8 Incidental Take Statement

Section 9 of the ESA and Federal regulations pursuant to section 4(d) of the ESA prohibit the
take of endangered and threatened species, respectively, without a special exemption. Take is
defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt
to engage in any such conduct. Harm is further defined by regulation to include significant
habitat modification or degradation that actually kills or injures fish or wildlife by significantly
impairing essential behavioral patterns, including breeding, spawning, rearing, migrating,
feeding, or sheltering (50 CFR 222.102). Incidental take is defined by regulation as takings
that result from, but are not the purpose of, carrying out an otherwise lawful activity conducted
by the Federal agency or applicant (50 CFR 402.02). Section 7(b)(4) and section 7(o)(2) provide
that taking that is incidental to an otherwise lawful agency action is not considered to be
prohibited taking under the ESA if that action is performed in compliance with the terms and
conditions of this incidental take statement.

2.8.1 Amount or Extent of Take

In the biological opinion, NMFS determined that incidental take would occur as follows:

Each year (2016-2020), up to 50 juvenile CCC steelhead and 5 juvenile CCC coho salmon are
likely to be captured and relocated prior to dewatering the sediment removal site. Of the fish
present, three (3) may be unintentionally injured or killed during relocation and dewatering.
Incidental take will have been exceeded if more than 55 juvenile salmonids are captured or more
than three (3) juvenile salmonids are injured or killed each year.

2.8.2 Effect of the Take

In the biological opinion, NMFS determined that the amount or extent of anticipated take,
coupled with other effects of the proposed action, is not likely to result in jeopardy to the species
or destruction or adverse modification of critical habitat.

2.8.3 Reasonable and Prudent Measures

Reasonable and prudent measures are nondiscretionary measures that are necessary or
appropriate to minimize the impact of the amount or extent of incidental take (50 CFR 402.02).

NMFS believes the following reasonable and prudent measures are necessary and appropriate to
minimize take of CCC steelhead and CCC coho salmon:

1. Undertake measures to ensure that harm and mortality to listed salmonids resulting
from fish relocation and dewatering activities is low.

2. Prepare and submit reports which summarize the effects of sediment removal, fish
relocation and dewatering activities, and post-sediment removal site performance.

27
2.8.4 Terms and Conditions

The terms and conditions described below are non-discretionary, and the Corps and/ or Syar
Industries or their agents must comply with them in order to implement the reasonable and
prudent measures (50 CFR 402.14). The Corps and County of San Mateo, Department of Public
Works have a continuing duty to monitor the impacts of incidental take and must report the
progress of the action and its impact on the species as specified in this incidental take statement
(50 CFR 402.14). If the entity to whom a term and condition is directed does not comply with
the following terms and conditions, protective coverage for the proposed action would likely
lapse.

1. The following terms and conditions implement Reasonable and Prudent Measure 1:

a. The County of San Mateo, Department of Public Works will retain qualified
biologists with expertise in the areas of anadromous salmonid biology, including
handling, collecting, and relocating salmonids; salmonid/habitat relationships; and
biological monitoring of salmonids. The County of San Mateo, Department of Public
Works will ensure that all biologists working on the project are qualified to conduct
fish collections in a manner which minimizes all potential risks to steelhead.

b. The biologists will monitor the placement and removal of cofferdams during
dewatering of the creek channel to ensure any adverse effects to salmonids are
minimized. The biologists will be on site during all dewatering events to capture,
handle, and safely relocate steelhead. The County, or the biologists, will notify
NMFS biologist, William Stevens at (707) 575-6066 or William.Stevens@noaa.gov
one week prior to capture activities in order to provide an opportunity for NMFS staff
to observe the activities.

c. Juvenile salmonids will be handled with extreme care and kept in water to the
maximum extent possible during rescue activities. All captured fish must be kept in
cool, shaded, and aerated water protected from excessive noise, jostling, or
overcrowding any time they are not in the stream, and fish will not be removed from
this water except when released. To avoid predation, the biologists will have at least
two containers and segregate young-of-the-year fish from larger age-classes and other
potential predators. Captured steelhead will be relocated as soon as possible to a
suitable instream location in which suitable habitat conditions are present to allow for
adequate survival for transported fish and fish already present.

d. If any salmonids are found dead or injured, the biologist will contact NMFS biologist
William Stevens by phone immediately at (707) 575-6066 or the NMFS North-
Central Coast Office in Santa Rosa at (707) 575-6050. The purpose of the contact is
to review the activities resulting in the take and to determine if additional protective
measures are required. All salmonid mortalities will be retained, placed in an
appropriately-sized sealable plastic bag, labeled with the date and location, fork
length, and be frozen as soon as possible. Frozen samples will be retained by the
biologist until specific instructions are provided by NMFS. The biologist may not

28
 transfer biological samples to anyone other than the NMFS North-Central Coast
Office without obtaining prior written approval from a North-Central Coast Office
supervisor.

2. The following terms and conditions implement Reasonable and Prudent Measure 2:

a. The County of San Mateo, Department of Public Works will prepare and submit a
report which summarize the effects of the project. This will be done to validate
assumptions and considerations made by NMFS and County of San Mateo,
Department of Public Works.

i. Annual Maintenance Plan. On January 15th of the year immediately

following sediment removal activities, the County shall provide their Annual
Maintenance Plan to NMFS. This plan shall include an evaluation on the
effectiveness of sediment removal activities on flooding, including the amount of
sediment removed.

ii. Fish Relocation. On January 15th of the year immediately following sediment
removal activities, the County shall provide a report to NMFS which includes a
description of the location from which fish were removed and the release site
including photographs; the date and time of the relocation effort; a description of
the equipment and methods used to collect, hold, and transport salmonids; the
number of fish relocated by species; the number of fish (by species) injured or
killed and a brief narrative of the circumstances surrounding steelhead injuries or
mortalities; and a description of any problems which may have arisen during the
relocation activities and a statement as to whether or not the activities had any
unforeseen effects.

b. All reports, plans or notifications required for the above terms and conditions shall be
sent to:

National Marine Fisheries Service, North-Central Coast Office

West Coast Region, Attn: William Stevens
777 Sonoma Avenue, Room 325
Santa Rosa, California 95404
707-575-6066
William.Stevens@noaa.gov

2.9 Conservation Recommendations

Section 7(a) (1) of the ESA directs Federal agencies to use their authorities to further the
purposes of the ESA by carrying out conservation programs for the benefit of the threatened and
endangered species. Specifically, conservation recommendations are suggestions regarding
discretionary measures to minimize or avoid adverse effects of a proposed action on listed
species or critical habitat or regarding the development of information (50 CFR 402.02).

29
The project is proposed with conservation measures and active enhancement of fisheries habitat
for ESA listed species. Thus no further conservation measures are recommended for this
specific project.

2.10 Reinitiation of Consultation

This concludes formal consultation for the Corps proposed issuance of a permit to County of
San Mateo, Department of Public Works for their proposed Butano Creek at Pescadero Creek
Road Sediment Removal Project located near Pescadero, in San Mateo County, California. As
50 CFR 402.16 states, reinitiation of formal consultation is required where discretionary Federal
agency involvement or control over the action has been retained or is authorized by law and if:
(1) the amount or extent of incidental taking specified in the incidental take statement is
exceeded, (2) new information reveals effects of the agency action that may affect listed species
or critical habitat in a manner or to an extent not considered in this opinion, (3) the agency action
is subsequently modified in a manner that causes an effect to the listed species or critical habitat
that was not considered in this opinion, or (4) a new species is listed or critical habitat designated
that may be affected by the action.

3. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT CONSULTATION

Section 305(b) of the MSA directs Federal agencies to consult with NMFS on all actions or
proposed actions that may adversely affect EFH. The MSA (section 3) defines EFH as those
waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.
Adverse effect means any impact that reduces quality or quantity of EFH, and may include direct
or indirect physical, chemical, or biological alteration of the waters or substrate and loss of (or
injury to) benthic organisms, prey species and their habitat, and other ecosystem components, if
such modifications reduce the quality or quantity of EFH. Adverse effects on EFH may result
from actions occurring within EFH or outside of it and may include site-specific or EFH-wide
impacts, including individual, cumulative, or synergistic consequences of actions (50 CFR
600.810). Section 305(b) also requires NMFS to recommend measures that can be taken by the
action agency to conserve EFH.

This analysis is based, in part, on the EFH assessment provided by the Corps and descriptions of
EFH contained in the Pacific Coast Salmon Fishery Management Plan (PFMC 1999) developed
by the Pacific Fishery Management Council and approved by the Secretary of Commerce.

3.1 Essential Fish Habitat Affected by the Project

EFH managed under the Pacific Coast Salmon Fishery Management Plan may be adversely
affected by the project.

30
3.2 Adverse Effects on Essential Fish Habitat

Adverse effects to EFH for Pacific salmon will occur through temporarily impaired water quality
and disturbance of benthic biological community, including removal of benthic prey organisms.

3.2.1. Water quality

As described in section 2.4.3 and 2.4.4 of the biological opinion, in-stream and near-stream
activities associated with sediment removal may cause temporary increases in turbidity, NMFS
anticipates only short-term changes to water quality conditions will occur during proposed
activities (e.g., construction and removal of cofferdams and the initial re-wetting of the channel
following the removal of the diversion). Water quality alteration is expected to be limited to the
immediate area of sediment removal activities and extend approximately 200 feet downstream of
the project site. It is expected that fish species encountering the altered water quality conditions
will react behaviorally and either move away from or avoid them. These effects are expected to
be temporary and there is ample area for fish to move to downstream of the action area.

Vegetation removal can affect stream-dwelling salmonids by increasing sun exposure and
increasing water temperature, depressing allochthanous food input, and cause erosion of newly
exposed soil. However, the low number of trees removed during the Project sediment removal
events are is unlikely to significantly affect stream temperature or food input, considering the
densely vegetated and wooded riparian wetland within, upstream, and downstream of the Project
site. Soil erosion will be minimized by hydroseeding and appropriate sediment controls methods
(i.e., fiber rolls, silt fences [Table 2 in the April 2015 Butano Creek at Pescadero Creek Road
Sediment Removal Project: Attachment A Supplemental Information]). Additionally, native
willow and alder trees surrounding the sediment removal area are expected to grow rapidly and
re-establish in disturbed areas. The effects to water quality are expected to be temporary.

3.2.2. Benthic disturbance

As described in sections 2.4.2 and 2.4.5 of the biological opinion, the Project proposes to remove
sediment and vegetation. Disturbance to benthic habitat from sediment removal and channel
dewatering may result in the direct removal of prey resources. NMFS expects the loss of
macroinvertebrates as a result of dewatering activities and sediment removal is likely to result in
the temporary loss of prey organisms for Pacific salmonids. Based on the rapid recolonization
by macroinvertebrates and because food is expected to be available via drift, NMFS will assume
full recovery of prey resources within approximately two months following sediment removal
and dewatering activities.

3.3 Essential Fish Habitat Conservation Recommendations

Because the project is designed to avoid or minimize potential adverse effects to EFH, no EFH
conservation recommendations are provided.

31
3.4 Supplemental Consultation

The Corps must reinitiate EFH consultation with NMFS if the proposed action is substantially
revised in a way that may adversely affect EFH, or if new information becomes available that
affects the basis for NMFS EFH Conservation Recommendations (50 CFR 600.920(l)).

4. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW

The Data Quality Act (DQA) specifies three components contributing to the quality of a
document. They are utility, integrity, and objectivity. This section of the opinion addresses these
DQA components, documents compliance with the DQA, and certifies that this opinion has
undergone pre-dissemination review.

4.1 Utility

Utility principally refers to ensuring that the information contained in this consultation is helpful,
serviceable, and beneficial to the intended users. The intended users of this opinion are the
Corps. Other interested users could include County of San Mateo, Department of Public Works,
California Department of Fish and Wildlife, and California Department of Parks and Recreation.
Individual copies of this opinion were provided to the Corps and County of San Mateo,
Department of Public Works. This opinion will be posted on the Public Consultation Tracking
System web site (https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts ). The format and naming
adheres to conventional standards for style.

4.2 Integrity

This consultation was completed on a computer system managed by NMFS in accordance with
relevant information technology security policies and standards set out in Appendix III, Security
of Automated Information Resources, Office of Management and Budget Circular A-130; the
Computer Security Act; and the Government Information Security Reform Act.

4.3 Objectivity

Information Product Category: Natural Resource Plan

Standards: This consultation and supporting documents are clear, concise, complete, and
unbiased; and were developed using commonly accepted scientific research methods. They
adhere to published standards including the NMFS ESA Consultation Handbook, ESA
regulations, 50 CFR 402.01 et seq., and the MSA implementing regulations regarding EFH, at
50 CFR 600.

Best Available Information: This consultation and supporting documents use the best available
information, as referenced in the References section. The analyses in this opinion and EFH
consultation contain more background on information sources and quality.

32
Referencing: All supporting materials, information, data and analyses are properly referenced,
consistent with standard scientific referencing style.

Review Process: This consultation was drafted by NMFS staff with training in ESA and MSA
implementation, and reviewed in accordance with West Coast Region ESA quality control and
assurance processes.

5. REFERENCES

Abdul-Aziz, O.I., N.J. Mantua, K.W. Myers. 2011. Potential climate change impacts on thermal
habitats of Pacific salmon (Oncorhynchus spp.) in the North Pacific Ocean and adjacent
seas. Canadian Journal of Fisheries and Aquatic Sciences 68(9):1660-1680.

Adams, P.B., M.J. Bowers, H.E. Fish, T.E. Laidig, and K.R. Silberberg. 1999. Historical and
current presence-absence of coho salmon (Oncorhynchus kisutch) in the Central
California Coast Evolutionarily Significant Unit. NMFS Administrative Report SC-99-
02. National Oceanic and Atmospheric Administration, National Marine Fisheries
Service, Southwest Fisheries Science Center, Tiburon, California. April, 1999.

Alexander, G. R., and E. A. Hansen. 1986. Sand bed load in a brook trout stream. North
American Journal of Fisheries Management 6:9-23.

Baker, P., and F. Reynolds. 1986. Life history, habitat requirements, and status of coho salmon
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Shapovalov, L., and A.C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo
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listed under the Endangered Species Act: Southwest. 2 February 2016 Report to National
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Magazine, February 2008, 72(1). 359-362.

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Waters, T.F., 1995. Sediment in streams: sources, biological effects, and control. American
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1995.

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Marine Fisheries Service. Southwest Fisheries Science Center. Santa Cruz, California.

5.1 Federal Register Notices Cited

61 FR 56138. 1996. National Marine Fisheries Service. Final rule: Endangered and threatened
species: threatened status for central California coho salmon evolutionarily significant
unit (ESU). Federal Register 61:56138-56149.

62 FR 43937. 1997. National Marine Fisheries Service. Final Rule: Listing of Several
Evolutionary Significant Units of West Coast Steelhead. Federal Register 62:43937-
43954. August 18, 1997.

64 FR 24049. 1999. National Marine Fisheries Service. Final Rule and Correction:
Designated Critical Habitat; Central California Coast and Southern Oregon/Northern
California Coasts Coho Salmon. Federal Register 64:24049-24062. May 5, 1999.

70 FR 37160. 2005. Final Rule: Endangered and Threatened Species: Final Listing
Determinations for 16 ESUs of West Coast Salmon, and Final 4(d) Protective
Regulations for Threatened Salmonid ESUs Designation of Critical Habitat for Seven
Evolutionarily Significant Units of Pacific Salmon and Steelhead in California. United
States Department of Commerce, National Oceanic and Atmospheric Administration,
National Marine Fisheries Service. Federal Register, Volume 70 pages 37160-37204.
June 28, 2005.

70 FR 52488. 2005. National Marine Fisheries Service. Final critical habitat designations for
19 West Coast salmon and steelhead ESUs. Federal Register 70:5248852627.
September 2, 2005.

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71 FR 834. 2006. National Marine Fisheries Service. Final Listing Determinations for Ten
Distinct Population Segments of West Coast Steelhead; Final Rule. Federal Register
71:834-862. January 5, 2006.

76 FR 76386. 2011. National Marine Fisheries Service. Endangered and Threatened Species;
5-Year Reviews for 4 Distinct Population Segments of Steelhead in California. December
7, 2011.

81 FR 7214. 2016. National Marine Fisheries Service. Rules and Regulations: Interagency
CooperationEndangered Species Act of 1973, as Amended; Definition of Destruction
or Adverse Modification of Critical Habitat. Final Rule. Federal Register, Vol. 81, No.
28. February 11, 2016. Effective March 14, 2016.

5.2 Personal Communication

Jahn, J. 2010. National Marine Fisheries Service.

Spence, B. 2016. Southwest Fisheries Science Center, National Marine Fisheries Service.

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