140P8621R0016_-_NMFS_Letter_excerpts_0001.pdf

Excerpts from NMFS letter 12/25/2021

Refer to NMFS No: WCRO-2020-03272

On November 25, 2020, NOAA’s National Marine Fisheries Service (NMFS) received your request for a written concurrence that the National Park Service’s (NPS) proposed replacement of the floating dock at the Scow Schooner Alma (Alma) in the San Francisco Maritime Historical Park is not likely to adversely affect species listed as threatened or endangered or critical habitats designated under the Endangered Species Act (ESA). This response to your request was prepared by NMFS pursuant to section 7(a)(2) of the ESA and implementing regulations at 50 CFR 402.

Thank you also for your request for consultation pursuant to the essential fish habitat (EFH) provisions in Section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act

(MSA) (16 U.S.C. 1855(b)) for this action. This review was pursuant to section 305(b) of the MSA, implementing regulations at 50 CFR 600.920, and agency guidance for use of the ESA consultation process to complete EFH consultation.

This letter underwent pre-dissemination review 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 within two weeks at NMFS’ Environmental Consultation Organizer

(ECO) at this link: [https://www.fisheries.noaa.gov/resource/tool-app/environmental-consultation-organizer-eco]. A complete record of this consultation is on file at NMFS North-Central Coast Office in Santa Rosa, California.

Consultation History

The NPS initiated informal consultation with NMFS by letter on November 25, 2020, and transmitted a biological assessment prepared by Anchor QEA, LLC by email on the same day. On

December 1, 2020, NMFS informed NPS by email that their request for consultation included species and critical habitat not found in this action area and clarified that longfin smelt (Spirinchus thaleichthys) is a state-listed species that is not managed by NMFS. NMFS also requested information regarding materials to be used in the proposed replacement dock. NPS responded via email on December 2, 2020, with information regarding materials for the proposed project. To clarify the species that may be affected by the project and NPS’ determinations of “not likely to adversely affect”, NPS sent NMFS an updated consultation request letter via email on December 9, 2020.

By email on January 14, 2021, NMFS requested additional information regarding the piles and installation methods for the replacement dock. NPS responded on January 15, 2021, with the requested information. Sufficient information was provided on January 15, 2021, for NMFS to initiate consultation.

Proposed Action and Action Area

The NPS is proposing to remove and replace the existing floating dock at the Alma with a concrete float, public access ramp, boarding gangway, and vessel access gangway. The proposed facility would provide continued public access to the Alma, an 1891 National Historic Landmark scow schooner.

The proposed project is located in San Francisco Bay at the end of Hyde Street Pier on the eastern side of Aquatic Park in San Francisco, California. The existing Alma Dock configuration includes two floating docks and a small floating connector dock. Of these existing components, the proposed project includes removal of the larger northwest floating dock and four 12-inch steel piles, as well as the small floating connector dock. These components would be replaced with an 80-foot by 16-foot floating dock supported by four 18-inch steel piles with 22-inch high-density polyethylene (HDPE) sleeves. A new 16-foot by 6-foot, 4-inch aluminum float gangway would be installed between the remaining existing dock and the new replacement dock. Access from the replacement dock to the

Alma would be provided by a new 5-foot by 5-foot gangway. The total overwater coverage area of existing dock components to be removed is 1,084 square feet. The replacement dock components would have an overwater coverage area of 1,406 square feet (i.e., net increase of 303 square feet of overwater structure). The new support piles will occupy approximately 11 square feet on the bay floor which is a net increase of 8 square feet.

Existing Alma Dock components would be disassembled using hand tools and would likely be removed using a small crane or excavator lift. Existing piles would either be pulled using a small crane or excavator or vibrated out using a vibratory hammer.

All new dock components would be prefabricated off site. New piles would be installed using a vibratory hammer, with the possible use of an impact hammer if hard obstacles are encountered that cannot be passed using a vibratory hammer. If an impact hammer is used, an air bubble curtain system will be deployed to attenuate underwater sound levels. It is anticipated that each of the four steel piles will require up to 6 hours to install and one pile will be installed per day (i.e., four days total). Installation of the replacement deck would occur using a small crane or excavator lift operating from the Hyde Street Pier and adjacent wooden floating dock, or from a barge operating in adjacent Bay waters. Fittings and auxiliary dock components (e.g., utilities) would be installed with hand tools.

All in-water construction (i.e., removing and replacing docks and piles) would be confined to the period between June 1 and November 30. NPS also proposes the following best management practices:

• Netting, sandbags, tarps, or other forms of barriers would be placed around staging areas to prevent debris from entering the water.

• All construction-related equipment would be inspected daily and maintained in good working order to minimize the potential for hazardous waste spills. Current hazardous material spill prevention and cleanup plans would be maintained on site. Hammers and other hydraulic attachments would be placed on plywood and covered with plastic or a comparable material prior to the onset of rain to prevent run-on and runoff.

• All debris and trash would be collected and disposed of in appropriate waste containers by the end of each construction day. Discharge of hazardous materials into the project site would be prohibited.

We considered, under the ESA whether or not the proposed action would cause any other activities and determined that it would not.

The Alma Dock project site is located in the San Francisco Maritime National Historical Park at the end of the Hyde Street Pier on the eastern side of Aquatic Park in San Francisco, California. The

Hyde Street Pier is a historic ferry pier and extends north from a heavily developed shoreline area with commercial and recreational amenities. The action area for the project consists of the northern terminus of the Hyde Street Pier and the surrounding San Francisco Bay waters extending 1,500 feet from the pier where elevated sound levels during pile driving may occur. The action area is partially enclosed and separated from the open waters of San Francisco Bay by a reinforced concrete breakwater constructed by the Army Corps of Engineers in 1986 to protect Fisherman’s Wharf from wave damage. Aquatic habitat within this area is shallow subtidal open water, with water depths ranging from approximately 5 to 10 feet at mean lower low water (MLLW). There are many concrete and wooden piles in the action area and the benthic habitat consists of soft bottom sediments. These habitat features likely support a diverse assemblage of fish, invertebrate, and algal species that are common in San Francisco Bay and can be a prey resource for many fish species (Filice 1953, De

Martini 1969, Donat III 1975, Moyle 2002, Watters et al. 2004, Thompson et al. 2007, Kritzer et al.

2016).

Background and Action Agency’s Effects Determination

The NPS has determined the proposed action may affect, but is not likely to adversely affect

Sacramento River winter-run (SRWR) Chinook salmon, Central Valley spring-run (CVSR) Chinook salmon, Central Valley (CV) steelhead, Central California Coast (CCC) steelhead, Southern Distinct

Population Segment (DPS) of North American green sturgeon, and designated critical habitats. The

NPS finding of not likely to adversely affect is based on the project’s proposed avoidance measures, brief period of construction, and temporary nature of impacts.

Available information indicates the following listed species (Evolutionarily Significant Units [ESU] or DPS) under the jurisdiction of NMFS may be affected by the proposed project:

Sacramento River winter-run Chinook salmon ESU (Oncorhynchus tshawytscha) endangered (70 FR 37160; June 28, 2005) critical habitat (58 FR 33212; June 16, 1993);

Central Valley spring-run Chinook salmon ESU (Oncorhynchus tshawytscha) threatened (70 FR 37160; June 28, 2005);

California Central Valley steelhead DPS (Oncorhynchus mykiss) threatened (71 FR 834; January 5, 2006);

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

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

The life history of steelhead is summarized in Busby et al. (1996) and Chinook salmon life history is summarized in Myers et al. (1998). SRWR Chinook salmon, CVSR Chinook salmon, CV steelhead, and CCC steelhead use Central San Francisco Bay primarily as a migration corridor. These anadromous salmonids pass downstream through the San Francisco Bay estuary to rear as juveniles in the ocean or to upstream areas to spawn as adults. Their migrations take place in the winter and spring months.

Adams et al. (2002), NMFS (2005), and (NMFS 2015) summarize the life history of green sturgeon in California. The Southern DPS of North American green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River. As juvenile green sturgeon age, they migrate downstream and live in the lower delta and bays, spending from three to four years there before entering the ocean. Green sturgeon likely optimize their growth opportunities in summer by foraging in the relatively warm waters of estuaries (Moser and Lindley 2007). Green sturgeon forage on benthic prey items throughout the estuary, notably shallow tidal flats dominated by burrowing shrimp and other benthic prey items (Dumbauld et al. 2008). Green sturgeon juveniles, subadults, and adults

(pre-and post-spawning) are present in San Francisco Bay at various times throughout the entire year.

Regarding EFH, the NPS determined that the proposed project may affect EFH, but that these impacts would be temporary and minimal. The project area is located within an area identified as

EFH for various life stages of fish species managed with the Pacific Coast Salmon Fishery

Management Plans (FMP), the Pacific Groundfish FMP, and the Coastal Pelagic FMP. The project area is also within an area designated as Habitat Areas of Particular Concern (HAPC) for various federally-managed fish species within the Pacific Groundfish and Pacific Salmon FMPs.1

1 For more information on HAPCs designated under the Groundfish and Salmon FMPs, please see page 102 of the

Groundfish FMP at http://www.pcouncil.org/wp-content/uploads/2017/03/GF_FMP_FinalThruA27-Aug2016.pdf, and page 6 of the Salmon FMP Appendix A at http://www.pcouncil.org/wp-content/uploads/Salmon_EFH_

Appendix_A_FINAL_September-25.pdf.

ENDANGERED SPECIES ACT

Effects of the Action

Under the ESA, “effects of the action” are all consequences to listed species or critical habitat that are caused by the proposed action, including the consequences of other activities that are caused by the proposed action. A consequence is caused by the proposed action if it would not occur but for the proposed action and it is reasonably certain to occur. Effects of the action may occur later in time and may include consequences occurring outside the immediate area involved in the action (50 CFR

402.02). In our analysis, which describes the effects of the proposed action, we considered 50 CFR

402.17(a) and (b). When evaluating whether the proposed action is not likely to adversely affect listed species or critical habitat, NMFS considers whether the effects are expected to be completely beneficial, insignificant, or discountable. Completely beneficial effects are contemporaneous positive effects without any adverse effects to the species or critical habitat. Insignificant effects relate to the size of the impact and should never reach the scale where take occurs. Effects are considered discountable if they are extremely unlikely to occur.

The effects of the proposed action are reasonably likely to include degradation of water quality, elevated underwater sound, and benthic disturbance during piling removal/installation activities. By restricting in-water work to the period between June 1 and November 30, the proposed work schedule avoids the migration periods of listed anadromous salmonids in this portion of Central San

Francisco Bay (Fukushima and Lesh 1998). Thus, NMFS anticipates listed salmonids will not be present in the action area at the end of the Hyde Street Pier during the construction period. Any construction-related effects to SRWR Chinook salmon, CVSR Chinook salmon, CV steelhead, and

CCC steelhead are anticipated to be discountable. Threatened green sturgeon are known to occur within San Francisco Bay year-round. Juvenile, sub-adult, or adult Southern DPS green sturgeon may be in the action area during construction activities and consequently, subject to potential project construction effects.

During piling removal and installation, disturbance of bottom sediments is likely to generate increased levels of turbidity in the water column, which can affect fish in a variety of ways. High levels of turbidity can affect listed fish species by disrupting normal feeding behavior, reducing growth rates, increasing stress levels, and reducing respiratory functions. If turbidity remains high for an extended period of time, the primary productivity of an aquatic area may be reduced (Cloern

1987) and fish may suffer reduced feeding ability and be prone to fish gill injury (Benfield and

Minello 1996, Nightingale and Simenstad 2001). Due to the brief duration of pile driving by this project (i.e. four days) and observations of similar pile removal/installation activities in San

Francisco Bay, increased levels of suspended sediment and turbidity are expected to be minor, localized, and short-term. Strong tidal currents in the action area are anticipated to rapidly return elevated levels of turbidity in the water column to background levels after work ceases. Green sturgeon are adapted to living in estuaries with fine sediment bottoms and are tolerant of levels of turbidity that exceed levels expected to result from this project. For these reasons, the potential effects of minor and localized areas of elevated turbidity associated with removal and installation of pilings at the Alma Dock are expected to be insignificant to green sturgeon.

Additionally, the project’s removal and installation of steel piles may effect green sturgeon through exposure to elevated levels of underwater sound. The NPS plans to use a vibratory hammer to install the four new 18-inch steel piles; however, an impact hammer may be used if hard obstacles are encountered. Monitoring of underwater sound levels associated with vibratory hammer activities have been performed previously for pile installation projects in San Francisco Bay. Based on hydroacoustic data collected from projects using vibratory hammers to install and remove piles

(Buehler et al, 2015), sound pressure levels generated by this project’s use of a vibratory hammer would not present a risk of physical injury or mortality to listed fish species.

In the unlikely event that hard obstacles are encountered during pile installation, an impact hammer may be used and green sturgeon could be exposed to considerably higher levels of underwater sound.

Available information indicates that fish may be injured or killed when exposed to high levels of underwater sound pressure waves generated from the use of impact hammers (Buehler et al. 2015).

To assess the potential effects of pile driving with an impact hammer, NMFS uses a dual metric criterion of 206 dB re one micropascal peak sound pressure level for any single strike and an accumulated sound exposure level (SEL) of 187 dB re one micropascal squared-second to correlate physical injury to fish greater than 2 grams in weight from underwater sound.

To attenuate underwater sound levels during use of an impact hammer, NPS proposes to use a bubble curtain. Bubble curtains have been shown to effectively reduce underwater sound levels as much as

20 dB; however, sound reductions of greater than 10 dB with attenuation systems cannot be reliably predicted (ICF Jones and Stokes and Illingworth and Rodkin, Inc. 2009). Based on the use of a bubble curtain during installation of 18-inch diameter steel piles with an impact hammer, this project is not expected to generate sound levels that will result in physical injury or mortality of listed fish.

However, green sturgeon that are present during pile driving may react behaviorally to elevated levels of underwater sound and temporarily disperse from the action area. Adequate water depths and carrying capacity in open water areas adjacent to the action area provide sufficient area for fish to disperse and forage. For the above reasons, the effects of elevated underwater sound levels and disturbance on threatened green sturgeon are expected to be insignificant.

The action area is located within designated critical habitat for CCC steelhead, SRWR Chinook salmon, and the Southern DPS of green sturgeon. The designation of critical habitat for these species uses the term primary constituent element (PCE) or essential features. The new critical habitat regulations (81 FR 7414) replace this term with physical or biological features (PBFs). This shift in terminology does not change the approach used in conducting our analysis, whether the original designation identified primary constituent elements, physical or biological features, or essential features. In this letter of concurrence, we use the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat.

The PBFs essential for the conservation of SRWR Chinook salmon relevant to estuarine areas include access from the Pacific Ocean to appropriate areas in the upper Sacramento River; habitat areas and adequate prey that are not contaminated; and access downstream so that juveniles can migrate from spawning grounds to San Francisco Bay and the Pacific Ocean. PBFs of designated critical habitat for CCC steelhead include estuarine areas free of obstruction with water quality, water quantity, and salinity conditions supporting juvenile and adult physiological transitions between fresh- and saltwater; natural cover such as submerged and overhanging large wood, aquatic vegetation, large rocks and boulders, and side channels; and juvenile and adult forage, including aquatic invertebrates and fishes, supporting growth and maturation. PBFs of critical habitat for the

Southern DPS of green sturgeon in estuarine areas include food resources, water flow, water quality, migratory corridor, water depth, and sediment quality.

During construction, critical habitat will be temporarily affected by potential increases in turbidity.

As discussed above, water quality effects in the form of increased turbidity are expected to be temporary and insignificant. Disturbance of sediments during the installation of the four steel piles could temporarily reduce benthic prey resources available for listed anadromous salmonids and green sturgeon. However, the area affected by these four piles is limited to approximately 11 square feet of sand/mud bottom and the net increase in the footprint of the pilings is approximately 5 square feet.

This small area of sand/mud bottom habitat lost is not expected to diminish foraging PBFs of critical habitat in the action area. Disturbed bottom sediments are expected to rapidly re-colonize with benthic invertebrates from adjacent sites due to the small area affected.

Impacts to critical habitat within the action area will also occur through an increase of the amount of overwater shading created by the replacement dock. The new Alma Dock will result in a net increase in overwater coverage of approximately 303 square feet. Overwater structures, such as docks and piers, result in shading of the water column and benthic habitats. Shading is known to reduce growth of submerged aquatic vegetation, decrease primary productivity, alter predator-prey interactions, change invertebrate assemblages, and reduce the density of benthic invertebrates (Helfman 1981, Glasby 1999, Struck et al. 2004, Stutes et al. 2006). Reduced light conditions found under an overwater structure also limit the ability of fishes, especially juveniles and larvae, to use visual cues for spatial orientation, prey capture, schooling, predator avoidance and migration (Hanson et al.

2003). For this project, the net increase in overwater shading is confined to a small area immediately adjacent to existing docks and submerged aquatic vegetation is not currently found within this area.

With frequent vessel traffic in the action area, this area is not likely to support submerged aquatic vegetation. Based on the highly modified condition of aquatic habitat in the action area and the small area affected by enlargement of overwater structure, the proposed project is not expected to degrade

PBFs of designated critical habitat for ESA-listed fish.

For the above reasons, the potential effects of this project on designated critical habitat are considered insignificant and are not expected to result in either a net change to existing habitat values in the action area or result in adverse impacts to designated critical habitat.

Conclusion

Based on this analysis, NMFS concurs with the NPS that the proposed action is not likely to adversely affect the subject listed species and designated critical habitats

Reinitiation of Consultation

Reinitiation of consultation is required and shall be requested by the NPS or by NMFS, where discretionary Federal involvement or control over the action has been retained or is authorized by law and (1) the proposed action causes take; (2) new information reveals effects of the action that may affect listed species or critical habitat in a manner or to an extent not previously considered; (3) the identified action is subsequently modified in a manner that causes an effect to the listed species or critical habitat that was not considered in the written concurrence; or (4) a new species is listed or critical habitat designated that may be affected by the identified action (50 CFR 402.16). This concludes the ESA consultation.

MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

Section 305(b) of the MSA directs Federal agencies to consult with NMFS on all actions or proposed actions that may adversely affect EFH. Under the MSA, this consultation is intended to promote the conservation of EFH as necessary to support sustainable fisheries and the managed species’ contribution to a healthy ecosystem. For the purposes of the MSA, EFH means “those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity”, and includes the associated physical, chemical, and biological properties that are used by fish (50 CFR 600.10).

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 may result from actions occurring within EFH or outside of it and may include direct, indirect, site-specific or habitat-wide impacts, including individual, cumulative, or synergistic consequences of actions (50 CFR 600.810).

Section 305(b) of the MSA also requires NMFS to recommend measures that can be taken by the action agency to conserve EFH. Such recommendations may include measures to avoid, minimize, mitigate, or otherwise offset the adverse effects of the action on EFH (50 CFR 600.905(b)).

NMFS determined the proposed actions would adversely affect EFH designated under the Pacific

Groundfish and the Coastal Pelagic FMPs due to localized increases in turbidity, disturbance of benthic habitat, and expanded area of overwater structure. As discussed above, adverse effects from turbidity and disturbance of the benthic community are expected be temporary and localized. The expanded area of overwater structure is limited to a small area (i.e., 303 square feet) along a highly developed pier. For these reasons, NMFS has no EFH conservation recommendations to avoid, minimize, mitigate, or otherwise offset the impact of the proposed action on EFH.

The NPS 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)). This concludes the

MSA consultation.