Pier 36 - Final Biological Opinion

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

Southwest Region 501 West Ocean Boulevard. Suite 4200 Long Beach. California 90802-4213

September 16, 2011

In response reply to:

2011 /00608

Lieutenant Colonel Torrey A. DiCiro U.S. Department of the Army San Francisco District Corps of Engineers 1455 Market Street, 16th Floor San Francisco, California 94103-1398

Dear Colonel DiCiro:

Thank you for your letter of February 16,2011, requesting consultation with NOAA's National Marine Fisheries Service (NMFS) pursuant to section 7 of the Endangered Species Act of 1973 (ESA), as amended (16 U.S.C. 1531 et seq.) for the u.S. Army Corps of Engineers' (Corps) and San Francisco Port's (Port) proposed Pier 36 Demolition/Brannan Street Wharf Project (Corps File No. 320786). The Corps proposes to demolish the existing Pier 36 and marginal wharf structure and authorize the Port to construct the new Brannon Street Wharf under the Nationwide Pennit provisions of Section 404 of the Clean Water Act.

The enclosed biological opinion is based on our review of the Corps' and Port's project and describes NMFS' analysis of potential effects on threatened Central California Coast (CCC) steel head distinct population segment (Oncorhynchus mykiss) (DPS), the Southern DPS of threatened North American green sturgeon (Acipenser medirostris) and their designated critical habitats in accordance with section 7 of the ESA. Threatened CCC steelhead and threatened North American green sturgeon are present within the project's action area and Central San Francisco Bay is designated critical habitat for these species. In the enclosed biological opinion, NMFS concludes that the project is not likely to jeopardize the continued existence of CCC steelhead or southern DPS green sturgeon. NMFS has also concluded the proposed project is not likely to result in the destruction or adverse modification of critical habitat for CCC steel head or green sturgeon. However, NMFS anticipates take of CCC steelhead and southern DPS green sturgeon may occur as a result of project construction. An incidental take statement with non discretionary tenns and conditions is included with the enclosed draft biological opinion.

Please contact Amanda Morrison at (707) 575-6083 if you have any questions concerning this section 7 consultation, or if you require additional information.

Sincerely, f,v Rodney R. McInnis Regional Administrator

Enclosure cc: Chris Yates, NMFS Long Beach, CA Tessa Bernhardt, Corps Envirorunental Section A, San Francisco, CA Chuck Armor, CDFG Bay Delta Region, Napa, California Ryan Olah, FWS, Sacramento, California Copy to File 151422SWR2011 SR00130

Enclosure

BIOLOGICAL OPINION

ACTION AGENCY: U.S. Army Corps of Engineers, Environmental Planning Section A, San Francisco District

ACTION: Pier 36 Demolition/Brannan Street Wharf Project in San Francisco, California.

CONSULTATION

CONDUCTED BY: National Marine Fisheries Service, Southwest Region

FILE NUMBER: 2011/00130

DATE ISSUED: September 16, 2011

I. CONSULTATION HISTORY

The U.S. Army Corps of Engineers (Corps) contacted the North Central Coast Office of NOAA’s National Marine Fisheries Service (NMFS) in Santa Rosa by telephone on November 30, 2009, regarding the Pier 36 Demolition and Brannan Street Wharf Project. They asked about the Section 7 consultation process and who would be the NMFS contact for Essential Fish Habitat (EFH) related questions.

On December 11, 2009, the Port of San Francisco (Port) hosted a conference call with NMFS and the Corps to discuss the Corps and Port’s draft project description. NMFS provided information on the potential impacts to species and what information the Corps should provide in their Biological Assessment to ensure they submit a complete consultation package. NMFS also provided the Corps and the Port information on the federally listed species that occur in the action area, however, the Corps requested a formal species list from NMFS in January 2011.

On June 24, 2010, the Port hosted a conference call with NMFS and the Corps to discuss what information the Corps should include in their biological assessment. Specific topics discussed were related to what resources are available to assist the Corps in preparing their pile driving impact analysis, the marine mammal take permit process, what types of figures would be helpful in illustrating the project’s area of cumulative impacts, and whether there were pile driving work windows in the Bay to avoid impacts to green sturgeon.

By letter dated January 5, 2011, to NMFS the Corps requested a list of federally-listed species and critical habitat that may be affected by the proposed project. By letter dated January 13, 2011, NMFS provided the Corps a list of federally listed threatened or endangered species or critical habitat that may be affected by the Pier 36/Brannan Street Wharf Project.

On January 24, 2011, the Port hosted a conference call with NMFS and the Corps to discuss the project timeline, pile driving sound analysis, contaminants in the action area, revisions to the project description, and useful information to include in the Biological Assessment, such as aerial photographs of the action area.

By letter dated February 16, 2011, the Corps requested initiation of formal section 7 consultation with NMFS regarding the Corps’ proposed demolition of Pier 36 and construction of the new Brannon Street Wharf. The Corps’ initiation request included the Biological Assessment/Essential Fish Habitat Assessment prepared by the Corps, dated January 2011, with appendices. The Corps determined the proposed project is likely to adversely affect Central California Coast (CCC) steelhead, but is not likely to adversely affect green sturgeon. The Corps also determined that the project is not likely to adversely modify critical habitat for CCC steelhead or green sturgeon.

NMFS received the Corps’ February 16, 2011, letter on February 25, 2011. Upon review of the Corps’ initiation package, NMFS determined that it contained the information necessary to initiate consultation on February 28, 2011.

NMFS issued a draft biological opinion to the Corps on August 11, 2011. By letter dated September 12, 2011, the Corps informed NMFS that they had no comments on the draft biological opinion

II. DESCRIPTION OF THE PROPOSED ACTION

The Corps proposes to demolish the existing Pier 36 and marginal wharf along San Francisco’s waterfront. Pier 36 is located along the Embarcadero (waterfront street) between Piers 30-32 and Pier 38, adjacent to Central San Francisco Bay, south of the San Francisco Bay Bridge, in San Francisco, California (Figure 1). Since the Corps will be conducting this demolition work, no Corps permit is required. For construction of the new Brannan Street Wharf by the Port, the Corps proposes to issue a permit under Section 404 of the Clean Water Act (Corps File No.

320786). Pier 36, along with the existing marginal wharf structure between Piers 30-32 and Pier 38, were condemned in 2004 due to the severely deteriorated deck structure and deteriorated pilings. The goal of the proposed project is to remove the existing degraded structures and construct a new, open-space, park along the San Francisco waterfront. The project will begin in January of 2012 and conclude in June of 2013. NMFS does not anticipate any interdependent or interrelated actions associated with the proposed action.

Figure 1

A. Descr

1. Demo

Pier 36 c wooden d structure

. Location o ription of P olition of Pie onsists of a decks and pi supported o of Pier 36, S

Proposed Pr er 36 and the

133,000-squ iles. Approx on 350 to 400

San Francis oject Design e Marginal W uare foot pile ximately 86, 0 concrete cy co Bay, Cal n and Const

Wharf e-supported 000 square f ylinders (or lifornia.

truction Ac concrete stru feet of Pier 3 caissons) wh ctivities ucture with d 36 is a steel hich are 42 i dilapidated and concrete inches in e diameter. The remaining 47,000 square feet section of Pier 36 is located at the Bay-end of the Pier and has collapsed. The Corps proposes to remove debris and creosote piles (approximately 350-400 creosote piles) that are part of the collapsed portion of Pier 36. In addition, on Pier 36, a 35,000 square feet warehouse building would be removed. The platform, supporting caissons and dilapidated structures of Pier 36 will be removed using a crane barge and excavator.

In addition to Pier 36, the Corps proposes to remove approximately 18,000 square feet of marginal wharf, located between the southern edge of Pier 32 and the northern edge of Pier 38.

The marginal wharf is a 20-foot-wide concrete and steel wharf supported on a mixture of concrete and timber piles that connects between the seawall and piers. The marginal wharf is approximately 940 feet in length and will be partially replaced by the new Brannon Street Wharf.

The Port also proposes repairs to an existing seawall on site. Seawall repair will include sealing cracks and patching spalls (chips) in the concrete wall.

The demolition work areas will include Pier 36, the marginal wharf, and a 40-foot-wide work zone into the Bay along the perimeter of Pier 36 and the marginal wharf. Demolition will be conducted from the water using a barge-mounted crane, and from land using a crawler crane.

Timber mats will be used to catch debris, and dump barges will be used to transport materials off site to an authorized upland disposal site. Caissons and piles will be removed by rocking them back and forth to free the belled end using an excavator, then lifted out using a crane barge.

Caissons and piles that break off at the mudline will be removed as is, leaving the bell in place.

Demolition of Pier 36 and the marginal wharf is scheduled to begin in January 2012, and be completed in May 2012. Demolition activities will be conducted during daylight hours,

2. Construction of the Brannon Street Wharf

The new Brannon Street Wharf will include 57,000 square feet of new public open space over San Francisco Bay with a pile-supported deck. It will be generally oriented in a north-south configuration, and connected to the Embarcadero Promenade. The northern end of the park would begin south of Piers 30-32, extending south for about 830 feet to a point south of Pier 36.

The wharf will have a wedge shape, starting from an approximately 10 feet width at its narrowest point and widening to approximately 140 feet at the southern end. An approximately 2400 square foot floating dock structure would extend outward into the Bay from the southern end of the wharf. This structure would provide a launch site for kayaks and other small, unpowered crafts.

Construction of the Brannon Street Wharf will require the installation of 261 steel and concrete piles and 57,000 square feet of new decking. The wharf structure will be supported by approximately 257 piles (116 24-inch diameter steel pipe piles and 141 24-inch diameter octagonal concrete piles) and the floating dock gangway will be supported by four 36-inch diameter steel piles. All piles will be driven to depths of more than 60 feet below the mudline in water depths ranging approximately 2 to 15 feet at mean low lower water (MLLW) and will be installed using a combination of impact and vibratory hammer driving methods. Pile driving will be done from the water using a barge-mounted marine crane and other construction activities will be primarily done from land. Construction of the new wharf is scheduled to begin in May 2012, and be completed in June 2013. In–water work will not extend beyond December 2012.

Construction will be conducted during daylight hours, except for a section of wharf near Pier 32, which will require double shifts to minimize impacts to traffic on the Embarcadero.

a. 24-inch octagonal concrete piles

Approximately 141 24-inch octagonal concrete piles will be driven by impact hammer into the Bay to support the new Brannon Street Wharf. The total time of pile driving for each pile is estimated to be 20 minutes in duration. During one work day, five to eight of the 24-inch octagonal concrete piles may be installed. If necessary, a water jet may be used to increase driving efficiency. Up to 800 blows from an impact hammer will occur for each pile, using a DelMag D46-32 diesel hammer, producing approximately 122,000 foot-pounds (ft-lbs) maximum energy per blow, at a rate of 1.5 seconds per blow (sec/blow) average.

b. 24-inch steel shell piles

Approximately 116 24-inch steel shell piles will be installed nearest the shoreline as support piles. During a work day, three to five piles may be installed. Each pile will be driven for 20 to 30 minutes. Installation will begin with approximately 8 minutes of vibratory pile driving, and finish with up to 300 blows from an impact hammer using a DelMag D46-32 diesel hammer, producing approximately 122,000 ft-lbs maximum energy per blow, at a rate of 1.5 sec/blow average.

c. 36-inch steel shell piles

Installation of the floating dock will require the placement of four 36-inch steel shell piles. It is estimated that each pile will be driven in 20 to 30 minutes. All four of these piles will be installed in one work day. Installation will begin with 5 to 15 minutes of vibratory driving, and finish with approximately 600 blows from a DelMag D62-22 diesel hammer, producing approximately 165,000 ft-lbs maximum energy, at a rate of 1.5 sec/blow.

3. Measures to Protect Listed Species and Critical Habitat

The Corps has proposed best management practices applicable to the control of sediment, hydrocarbon, and turbidity during construction. In addition to the general avoidance and minimization measures, measures specific to pile driving activities have been developed to reduce potential project effects on fish. The most pertinent of these measures are listed below.

Additional measures not listed below, may be found in detail on Pages 24-26 and Appendix E of the project’s biological assessment (2011).

To reduce peak noise levels during pile driving, vibratory hammers will be used to install all steel piles for the majority of the pile driving (e.g., up to the last 10 feet), then an impact hammer will need to be used to achieve the final required depth.

Pile driving with an impact hammer will employ a “soft start” technique. The soft start technique requires that the initial strikes of a piling with and impact hammer are not performed at full force, but a significantly reduced force and slowly build to full force over several strikes.

Unconfined bubble curtains will be used in deeper water to reduce noise levels.

Prior to the start of construction, the Port will develop a NMFS-approved sound attenuation and monitoring plan. This plan will provide details on the sound attenuation system and the methods used to monitor and verify sound levels during pile driving activities. The sound monitoring results will be made available to NMFS.

During demolition, the barges performing the work will be moored in a position to capture and contain the debris generated during the dismantlement of the building and wharf. In the event that debris does reach the Bay, personnel in work boats will immediate retrieve the debris for proper handling and disposal. All demolition debris will be disposed of at an authorized upland disposal site.

C. Description of the Action Area

The action area is defined as all areas affected directly or indirectly by the Federal action and not merely the immediate area involved (50 CFR 402.02). The proposed project is located in San Francisco City and County, California, in and along the western shore of the Central San Francisco Bay, just south of the Bay Bridge. Approximate site coordinates are 37.7834 degrees north latitude and 122.3878 degrees west longitude (WGS 84). The action area is approximately 70 acres and includes the area outside the project footprint that will be affected by noise and turbidity during pile removal, pile driving, and pier installation, and the areas that will be shaded by the new wharf structure. The potentially lethal effects of noise produced by the project are expected to extend up to approximately 355 meters (1,171 feet) radial distance from where the floating dock will be located, which is near the shoreline at Pier 36 (Figure 2).

Figure 2 355 mete

III. ANA

A. Jeopa

In accord on four c Populatio condition

2. Area wher er radius fro

ALYTICAL

ardy Analy dance with p components:

on Segment’ ns, the factor re potential om the shor

L FRAMEW

sis policy and re

(1) the Statu

’s (DPS) and rs responsibl ly lethal eff reline).

WORK

gulation, the us of the Spe d the North A le for that co fects to fish e jeopardy an ecies, which American gr ondition, and may be exp nalysis in th h evaluates th reen sturgeon d the species perienced (a his biological he CCC stee n southern D s’ likelihood approximate l opinion rel elhead Distin DPS’s range-of both surv ely lies nct -wide vival and recovery; (2) the Environmental Baseline, which evaluates the condition of the listed species in the action area, the factors responsible for that condition, and the relationship of the action area to the likelihood of both survival and recovery of the listed species; (3) the Effects of the Action, which determines the direct and indirect effects of the proposed Federal action and the effects of any interrelated or interdependent activities on the species in the action area; and (4) Cumulative Effects, which evaluates the effects of future, non-Federal activities in the action area on the species.

The jeopardy determination is made by adding the effects of the proposed Federal action and any Cumulative Effects to the Environmental Baseline and then determining if the resulting changes in species status in the action area are likely to cause an appreciable reduction in the likelihood of both the survival and recovery of the listed species in the wild.

The jeopardy analysis in this biological opinion places an emphasis on the range-wide likelihood of both survival and recovery of the listed species and the role of the action area in the survival and recovery of the listed species. The significance of the effects of the proposed Federal action is considered in this context, taken together with cumulative effects, for purposes of making the jeopardy determination. We use a hierarchical approach that focuses first on whether or not the effects on steelhead and green sturgeon in the action area will impact their respective population.

If the populations will be impacted, we assess whether this impact is likely to affect the ability of the populations to support the survival and recovery of the DPS.

B. Adverse Modification Determination

This Biological Opinion does not rely on the regulatory definition of destruction or adverse modification of critical habitat at 50 CPR 402.02.1 Instead, we have relied upon the statutory provisions of the ESA to complete the following analysis with respect to critical habitat.

The adverse modification analysis in this Biological Opinion relies on four components: (1) the Status of Critical Habitat, which evaluates the range-wide and watershed-wide condition of critical habitat for the CCC steelhead DPS and North American green sturgeon southern DPS in terms of primary constituent elements (PCEs – sites for spawning, rearing, and migration), the factors responsible for that condition, and the resulting conservation value of the critical habitat overall; (2) the Environmental Baseline, which evaluates the condition of critical habitat in the action area, the factors responsible for that condition, and the conservation value of the critical habitat in the action area; (3) the Effects of the Action, which determines the direct and indirect impacts of the proposed Federal action and the effects of any interrelated or interdependent activities on the PCEs in the action area and how that will influence the conservation value of affected critical habitat units; and (4) Cumulative Effects, which evaluates the effects of future, non-Federal activities in the action area on the PCEs and how that will influence the conservation value of affected critical habitat units.

For purposes of the adverse modification determination, we add the effects of the proposed Federal action on CCC steelhead and green sturgeon critical habitat in the action area, and any Cumulative Effects, to the Environmental Baseline and then determine if the resulting changes to

1 This regulatory definition has been invalidated by Federal Courts.

the conservation value of critical habitat in the action area are likely to cause an appreciable reduction in the conservation value of critical habitat range-wide. If the proposed action will negatively affect PCEs of critical habitat (sites for spawning, rearing, and migration) in the action area we then assess whether or not this reduction will impact the value of the DPS critical habitat designation as a whole.

C. Use of Best Available Scientific and Commercial Information

To conduct the assessment, NMFS examined an extensive amount of information from a variety of sources. Detailed background information on the biology and status of the listed species and critical habitat has been published in a number of documents including peer reviewed scientific journals, primary reference materials, and governmental and non-governmental reports.

Additional information regarding the effects of the project’s actions on the listed species in question, their anticipated response to these actions, and the environmental consequences of the actions as a whole was formulated from the aforementioned resources, the biological assessment for this project, and project meeting notes if applicable. Information was also provided in electronic mail messages (email), site visits, and telephone conversations between February 2011 and July 2011. For information that has been taken directly from published, citable documents, those citations have been referenced in the text and listed at the end of this document. A complete administrative record of this consultation is on file at the NMFS North Central Coast Office (Administrative Record Number 151422SWR2011SR00130).

IV. STATUS OF THE SPECIES AND CRITICAL HABITAT

This biological opinion analyzes the effects of the Corps’ Pier 36 Demolition/Brannan Street Wharf Project on the following Federally-listed species (Distinct Population Segments [DPS]) and designated critical habitat:

Central California Coast steelhead DPS (Oncorhynchus mykiss) threatened (January 5, 2006, 71 FR 834) critical habitat (September 2, 2005, 70 FR 52488)

North American green sturgeon southern DPS (Acipenser medirostris) threatened (April 7, 2006, 71 FR 17757) critical habitat (October 9, 2009; 74 FR 52300)

Salmonids that use Central Valley streams as their spawning grounds and freshwater rearing areas migrate through the Bay and occasionally stray into the Central Bay south of the Bay Bridge (Klimley et al. 2009; Jahn 2004). However, they generally show fidelity to deepwater migration corridors in the North Bay (Jahn 2004). NMFS expects that no salmonids belonging to Central Valley Evolutionary Significant Units (ESUs) or DPSs occur in the action area.

A. CCC Steelhead

1. General Description and Life History

Steelhead are anadromous forms of O. mykiss, spending some time in both fresh- and saltwater.

The older juvenile and adult life stages occur in the ocean, until the adults ascend freshwater streams to spawn. Unlike Pacific salmon, steelhead are iteroparous, or capable of spawning more than once before death (Busby et al. 1996). Although one-time spawners are the great majority, Shapolov and Taft (1954) reported that repeat spawners are relatively numerous (17.2 percent) in California streams. Eggs (laid in gravel nests called redds), alevins (gravel dwelling hatchlings), fry (juveniles newly emerged from stream gravels), and young juveniles all rear in freshwater until they become large enough to migrate to the ocean to finish rearing and maturing to adults. General reviews for steelhead in California document much variation in life history (Shapovalov and Taft 1954, Barnhart 1986, Busby et al. 1996, McEwan 2001). Although variation occurs, in coastal California steelhead usually live in freshwater for 1 to 2 years, then spend 1 to 3 years in the ocean before returning to their natal stream to spawn. Steelhead may spawn 1 to 4 times over their life. Adult steelhead typically migrate from the ocean to freshwater between December and April, peaking in January and February (Fukushima and Lesh 1998).

Juvenile steelhead migrate as smolts to the ocean from January through May, with peak migration occurring in April and May (Fukushima and Lesh 1998).

Steelhead fry rear in freshwater 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).

Steelhead, however, tend to use riffles and other habitats not strongly associated with cover during summer rearing more than other salmonids. Young steelhead feed on a wide variety of aquatic and terrestrial insects, and emerging fry are sometimes preyed upon by older juveniles.

Rearing steelhead juveniles prefer water temperatures of 7.2-14.4 degree Celsius (C) and have an upper lethal limit of about 25C (Barnhart 1986, Bjornn and Reiser 1991). However, they can survive in water up to 27C with saturated dissolved oxygen conditions and a plentiful food supply. Fluctuating diurnal water temperatures also aid in survivability of salmonids (Busby et

al. 1996).

Emigrating CCC steelhead use San Francisco Bay as a migration corridor to the ocean. Adult CCC steelhead migrate from the ocean to South San Francisco Bay tributary streams from December through April. Juvenile steelhead emigration from their South Bay natal streams occurs episodically during fall, winter, and spring months, and generally occurs during high flow events. Barnhart (1986) reported that steelhead smolts in California typically range in size from 140 to 210 millimeter (mm) (fork length). It is believed that the majority of juvenile steelhead transiting through the Bay migrate mainly within deeper areas of dredged ship channels opposed to the surrounding shallows (Klimley et al. 2009).

2. Status of CCC Steelhead DPS and Critical Habitat

In this opinion, NMFS assesses four population viability parameters to help us understand the status of CCC steelhead and the population’s ability to survive and recover. These population viability parameters are: abundance, population growth rate, spatial structure, and diversity (McElhany et al. 2000). While there is insufficient information to evaluate these population viability parameters in a thorough quantitative sense, NMFS has used existing information to determine the general condition of each population and factors responsible for the current status of each DPS.

We use these population viability parameters as surrogates for numbers, reproduction, and distribution, the criteria found within the regulatory definition of jeopardy (50 CFR 402.20). For example, the first three parameters are used as surrogates for numbers, reproduction, and distribution. We relate the fourth parameter, diversity, to all three regulatory criteria. Numbers, reproduction, and distribution are all affected when genetic or life history variability is lost or constrained resulting in reduced population resilience to environmental variation at local or landscape-level scales.

Historically, approximately 70 populations2 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). Recent estimates for the Russian River are on the order of 4,000 fish (NMFS 1997). Abundance estimates for smaller coastal streams in the DPS indicate low but stable levels with recent estimates for several streams (Lagunitas, Waddell, Scott, San Vincente, 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). Similar losses in genetic diversity in the Napa River may have resulted from out-of-basin and out-of-ESU releases of steelhead in the Napa River basin in the 1970s and 80s. These transfers included fish from the South Fork Eel River, San Lorenzo River, Mad River, Russian River, and the Sacramento River. 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 more detailed information on trends in CCC steelhead abundance, see: Busby et al. 1996, NMFS 1997, and Good et al. 2005, 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 DPS 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

2 Population as defined by Bjorkstedt et al. 2005 and McElhaney et al. 2000 as, in brief summary, a group of fish of the same species that spawns in a particular locality at a particular season and does not interbreed substantially with fish from any other group. Such fish groups may include more than one stream. These authors use this definition as a starting point from which they define four types of populations (not all of which are mentioned here).

extirpation. However, because CCC steelhead remain present in most streams 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 DPS or ESUs in worse condition. The most recent status review concludes that steelhead in the CCC steelhead DPS remain “likely to become endangered in the foreseeable future” (Good et al. 2005). On January 5, 2006, NMFS issued a final determination that the CCC steelhead DPS is a threatened species, as previously listed (71 FR 834).

A more recent viability assessment of CCC steelhead concluded that populations in watersheds that drain to San Francisco Bay are highly unlikely to be viable, and that the limited information available did not indicate that any other CCC steelhead populations could be demonstrated to be viable3 (Spence et al. 2008). Although there were average returns (based on the last ten years of data) of adult CCC steelhead during 2007/08, research monitoring data from the 2008/09 and 2009/10 adult CCC steelhead returns indicate a decline in returning adults across their range compared to the last ten years (Jeffrey Jahn, personal communication, 2010).

The condition of CCC steelhead 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 present depressed population conditions are, in part, the result of the following human-induced factors affecting critical habitat4: logging, agricultural and mining activities, urbanization, stream channelization, dams, wetland loss, and water withdrawals, including unscreened diversions for irrigation. Impacts of concern include alteration of streambank and channel morphology, alteration of water temperatures, loss of spawning and rearing habitat, fragmentation of habitat, loss of downstream recruitment of spawning gravels and large woody debris, degradation of water quality, removal of riparian vegetation resulting in increased streambank erosion, loss of shade (higher water temperatures) and loss of nutrient inputs (Busby et al. 1996, 70 FR 52488). Water development has drastically altered natural hydrologic cycles in many of the streams in the DPS. Alteration of flows results in migration delays, loss of suitable habitat due to dewatering and blockage; stranding of fish from rapid flow fluctuations; entrainment of juveniles into poorly screened or unscreened diversions, and increased water temperatures harmful to salmonids. Overall, current condition of CCC steelhead critical habitat is degraded, and does not provide the full extent of conservation value necessary for the recovery of the species.

B. Green Sturgeon

1. General Description and Life History

North American green sturgeon are the most widely distributed, and most marine-oriented of sturgeon species belonging to the family Acipenseridae. Like all sturgeon, North American green sturgeon are anadromous, long-lived, and a slow growing species (Adams et al. 2002).

Along the Pacific Coast, North American green sturgeon have been documented offshore from

3 Viable populations have a high probability of long-term persistence (> 100 years).

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

Ensenada, Mexico to the Bering Sea, Alaska and found in freshwater rivers from the Sacramento River to British Columbia (Moyle 2002).

Adult green sturgeon are believed to spawn every 3 to 5 years and generally exhibit fidelity to their spawning site. Green sturgeon reach sexual maturity only after several years of growth;

first spawning generally occurs at 15 years of age for males, and 17 years for females. Southern DPS green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River. The California Department of Fish and Game (CDFG) (2002) report southern DPS green sturgeon spawning occurs above Hamilton City and possibly as far upstream as Keswick Dam.

Adults typically begin their upstream spawning migrations into the San Francisco Bay by late February to early March, reach Knights Landing by April, and spawn between March and July (Heublein et al. 2009). Peak spawning is believed to occur between mid-April to mid-June.

Green sturgeon in the Sacramento River can display two outmigration strategies. Monitoring data reveals that post-spawned green sturgeon can leave the Sacramento River prior to September 1, or remain in the river for several additional months (Heublein et al. 2009).

Adult female green sturgeon produce between 60,000 and 140,000 eggs, depending on body size, with a mean egg diameter of 4.3 mm (Moyle et al. 1992, Van Eenennaam et al. 2001). Eggs are likely broadcast spawned over large cobble substrate where they settle into the spaces between the cobbles, but substrate can range from clean sand to bedrock (USFWS 2002). Like salmonids, green sturgeon require cool water temperatures for egg and larval development, with optimal temperatures ranging from 11 to 18˚C.

Juvenile green sturgeon spend from one to three years in freshwater before they enter the ocean (Nakamoto et al. 1995, Adams et al. 2002). Based on Klamath River age distribution work by Nakamoto et al. (1995), the majority of fish entering the ocean are between 200 and 600 mm in length which suggests they are 2 to 3 years of age. The low abundance of juveniles smaller than 200 mm in the Delta indicates juvenile southern DPS green sturgeon likely hold in the mainstem Sacramento River, as suggested by Kyndard et al. (2005). Laboratory studies, conducted by Allen and Cech, Jr. (2007), also indicated juveniles spend approximately the first six months in fresh to brackish water and then transition into salt water at about 1.5 years of age.

Both adult and juvenile green sturgeon are benthic feeders (Moyle 2002). Adult green sturgeon are believed to feed primarily upon benthic invertebrates such as clams, mysid and grass shrimp, and amphipods (Radtke 1966, Adams et al. 2002), and to some extent on fish. Adults captured in the Sacramento-San Joaquin Delta are known to feed on invertebrates such as shrimp, mollusks, amphipods, and additionally upon small fish (Adams et al. 2002). Juvenile green sturgeon in the San Francisco Bay have been shown to feed on opossum shrimp (Neomysis mercedie) and amphipods (Corophium spp.) (Moyle 2002).

Southern DPS green sturgeon are also known to inhabit nearshore marine waters, and are commonly observed in bays and estuaries. Kelly et al. (2007) studied the movement of six green sturgeon (one adult and five sub-adults) in the San Francisco Estuary (tagged in San Pablo Bay) and discovered while adults and sub-adults occupied shallow water depths, there were distinct directional movements. In contrast, when the fish exhibited non-directional movements, they remained close to the bottom. The movements were not found to be related to salinity, current, or temperature and the authors surmised they are related to food resource availability.

2. Status of Southern DPS Green Sturgeon and Critical Habitat

The southern DPS green sturgeon is considered vulnerable to catastrophic events due in part to a small estimated spawning population and drastic reductions in historically accessible spawning habitat. The precise population size of southern DPS green sturgeon is unknown, but it is likely to be much smaller than the northern DPS. Population abundance information concerning the southern DPS green sturgeon is described in the NMFS status reviews (Adams et al. 2002, NMFS 2005). Abundance information is limited, coming mainly from three sources: 1) incidental captures in the CDFG white sturgeon monitoring program, 2) fish monitoring efforts associated with two diversion facilities on the upper Sacramento River, and 3) fish salvage operations at the water export facilities on the Sacramento-San Joaquin Delta. These data are insufficient in a variety of ways (short time series, non-target species, etc.) and do not support more than a qualitative evaluation of changes in green sturgeon abundance.

Some population abundance information comes from incidental captures of southern DPS green sturgeon from the white sturgeon monitoring program by the CDFG sturgeon tagging program (CDFG 2002). CDFG (2002) utilizes a multiple-census or Peterson mark-recapture method to estimate the legal population of white sturgeon captures in trammel nets. By comparing ratios of white sturgeon to green sturgeon captures, CDFG provides estimates of adult and sub-adult southern DPS green sturgeon abundance. Estimated abundance between 1954 and 2001 ranged from 175 fish to more than 8,000 per year and averaged 1,509 fish per year. Unfortunately, there are many biases and errors associated with these data, and CDFG does not consider these estimates reliable. Fish monitoring efforts at the Red Bluff Diversion Dam (RBDD) and Glenn- Colusa Irrigation District (GCID) on the upper Sacramento River have captured between 0 and 2,068 juvenile southern DPS green sturgeon per year (Adams et al. 2002).

Green sturgeon salvage numbers are recorded at California State (1968-present) and Federal (1980-present) water export facilities on the Sacramento-San Joaquin Delta. The average number of southern DPS green sturgeon taken per year at the state facility prior to 1986 was 732;

from 1986 to 2001, the average per year was 47 (70 FR 17386). For the Federal facility, the average number prior to 1986 was 889; from 1986 to 2001 the average was 32 (70 FR 17386).

Additional analysis of southern DPS green sturgeon indicate a downward trend in the number of green sturgeon per acre-foot of exported water at state and Federal facilities since 1974 and 1983 respectively. Direct capture in salvage operations is a small component of the overall effect of water export facilities on southern DPS green sturgeon; entrained juvenile green sturgeon are exposed to potential high levels of predation by exotic predators, disruption in migratory behavior, and poor habitat quality. Delta water exports have likely contributed to negative trends in the abundance of migratory fish that utilize the delta, including the southern DPS green sturgeon. Catches of sub-adult and adult southern DPS green sturgeon by the Interagency Ecological Program (IEP) between 1996 and 2004 ranged from 1 to 212 green sturgeon per year (212 occurred in 2001), however, the portion of these captures consisting of southern DPS green sturgeon is unknown as the fish were primarily captured in San Pablo Bay which is known to consist of a mixture of northern and southern DPS green sturgeon.

Recent spawning population estimates using sibling based genetics by Israel (2006) indicates a maximum spawning population of 32 spawners in 2002, 64 in 2003, 44 in 2004, 92 in 2005, and 124 in 2006 above RBDD (with an average of 71). Based on the length and estimated age of post-larvae captured at RBDD (approximately two weeks of age) and GCID (downstream;

approximately three weeks of age), it appears the majority of southern DPS green sturgeon are spawning above RBDD.5

The most recent status review update concluded the southern DPS green sturgeon is likely to become endangered in the foreseeable future due to the substantial loss of spawning habitat, the concentration of a single spawning population in one section of the Sacramento River, and multiple other risks to the species such as stream flow management, degraded water quality, and introduced species (NMFS 2005). Based on this information, the southern DPS green sturgeon was listed as threatened on April 7, 2006 (71 FR 17757).

Critical habitat was designated for the southern DPS of green sturgeon on October 9, 2009 (74 FR 52300) and includes coastal United States marine waters within 60 fathoms depth from, and including, Monterey Bay, California, north to Cape Flattery, Washington, including the Strait of Juan de Fuca, Washington, to its United States boundary. The project’s action area (i.e., Central San Francisco Bay) is located within designated critical habitat for southern DPS green sturgeon.

Primary constituent elements of designated critical habitat in the action area include adequate food resources and foraging habitat; and the estuarine water column, which includes suitable depth, sediment, and water quality.

The current condition of critical habitat for the southern DPS of green sturgeon is degraded over its historical conditions. It does not provide the full extent of conservation values necessary for the recovery of the species, particularly in the upstream riverine habitat of the Sacramento River.

In particular, passage and water flow PCEs have been impacted by human actions, substantially altering the historical river characteristics in which the southern DPS of green sturgeon evolved.

In addition, the alterations to the Sacramento-San Joaquin River Delta may have a particularly strong impact on the survival and recruitment of juvenile green sturgeon due to their protracted rearing time in the delta and estuary. Loss of individuals during this phase of the life history of green sturgeon represents losses to multiple year classes rearing in the Delta, which can ultimately impact the potential population structure for decades to come.

C. Global Climate Change

Global climate change presents an additional potential threat to CCC steelhead, southern DPS green sturgeon, and their respective critical habitat. Modeling of climate change impacts in California suggests that average summer air temperatures are expected to increase (Lindley et al.

2007). Heat waves are expected to occur more often, and heat wave temperatures are likely to be higher (Hayhoe et al. 2004). Total precipitation in California may decline; critically dry years may increase (Lindley et al. 2007, Schneider 2007). The Sierra Nevada snow pack is likely to decrease by as much as 70 to 90 percent by the end of this century under the highest emission scenarios modeled (Luers et al. 2006). Wildfires are expected to increase in frequency and

5 There are many assumptions with this interpretation (i.e., equal sampling efficiency and distribution of post-larvae across channels) and this information should be considered cautiously.

magnitude, by as much as 55 percent under the medium emissions scenarios modeled (Luers et

al. 2006). Vegetative cover may also change, with decreases in evergreen conifer forest and increases in grasslands and mixed evergreen forests. The likely change in amount of rainfall in Northern and Central Coastal streams under various warming scenarios is less certain, although as noted above, total rainfall across the state is expected to decline. For the California North Coast, some models show large increases (75 percent to 200 percent) in rainfall amounts while other models show decreases of 15 percent to 30 percent (Hayhoe et al. 2004). Many of these changes are likely to further degrade CCC steelhead and southern DPS green sturgeon habitat by, for example, reducing stream flows during the summer and raising summer water temperatures.

The projections described above are for the mid to late 21st Century. In shorter time frames natural climate conditions are more likely to predominate (Cox and Stephenson 2007, Smith et

al. 2007).

V. ENVIRONMENTAL BASELINE

The environmental baseline is an analysis of the effects of past and ongoing human and natural factors leading to the current status of the species in the action area. 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).

The action area is in Central San Francisco Bay, just south of the Bay Bridge. San Francisco Bay is the largest estuary on the west coast of North America. Located about halfway up the California coast from the Mexican border, it is the natural exit point of 40 percent of California’s freshwater outflow. The climate is Mediterranean; most precipitation falls in winter and spring as rain throughout the Central Valley and as snow in the Sierra Nevada and Cascades. The freshwater outflow pattern is seasonal; highest outflow occurs in winter and spring. Current and wave patterns in the action area are largely generated by the tides interacting with the bottom and shoreline configurations. It also receives inputs from stormwater runoff, and wastewater from municipal and industrial sources that vary in volume depending on the location and seasonal weather patterns.

The action area consists of 1.5 acres of developed upland areas and 70 acres of open water areas in San Francisco Bay. Open water areas include the collapsed wharf extension area (1.08 acres) and 17 acres of Bay that are covered and shaded underneath Piers 30, 36, 38, and 40. Water within the action area varies in depth, ranging between 5 feet and, at the eastern edge, as deep as 55 feet (ft) at MLLW. Within the project footprint, water depths are shallow, around 7 ft MLLW on average. Benthic habitat in the action area includes Bay sand and mud. There is no rocky shoreline habitat within the action area. The transition zone between the upland areas to the subtidal zone consists of rip rap and retaining walls.

A. Status of Listed Species and Critical Habitat in the Action Area

1. CCC Steelhead

Data on steelhead presence in Central San Francisco Bay is limited. CDFG has sampled fish presence/absence at fixed stations in the Bay and Delta for over 25 years (IEP 2011). Data is comprised of otter trawl, midwater trawl, beach seine, and other gear catches at the various stations. The beach seine data cover only the years 1980 – 1986, and certain stations were added for other gear types. Very few steelhead were captured throughout these surveys, with less than 100 fish caught during all years sampled (Jahn 2004). All of the steelhead were caught in the northern and central portions of the Bay. The small number of captures of steelhead in during CDFG surveys is likely due to the small populations of CCC steelhead in south Bay streams (Jahn 2004). Based on this information, very few CCC steelhead are expected to be present in the action area. Those that do occur are expected to be actively migrating.

Available information suggests that salmonids depend very little on the Bay for rearing and migrate quickly through the estuary. Historically, the tidal marshes within San Francisco Bay provided a highly productive estuarine environment for juvenile steelhead. However, loss of habitat, changes in prey communities, and water-flow alterations and reductions, have degraded habitat, and limit the ability of the Bay to support juvenile rearing. McFarlane and Norton (2002) found that fall-run Chinook experienced little growth, depleted condition, and no accumulation of lipid energy reserves during the relatively limited time the fish spent transiting the 65-km length of the estuary.

Adults steelhead potentially occurring in the action area will be those fish that are transiting the Bay to their spawning grounds in Guadalupe River, Stevens Creek, San Francisquito Creek, Coyote Creek, Alameda Creek, and possibly…