NMFS LOC Reinitiation SF Bay Strategic Placement Pilot.pdf

September 29, 2023 Refer to NMFS No: WCRO-2023-02325

Dr. Tessa Beach Environmental Branch Chief U.S. Army Corps of Engineers San Francisco District 450 Golden Gate Avenue San Francisco, California 94102-3404

Re: Reinitiation of Endangered Species Act Section 7(a)(2) Concurrence Letter and

Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the 2023 San Francisco Bay Strategic Shallow-Water Placement Pilot Project

Dear Dr. Beach:

On September 15, 2023, NOAA’s National Marine Fisheries Service (NMFS) received your request for reinitiation of consultation pursuant to section 7 of the Endangered Species Act (ESA) for the San Francisco Bay Strategic Shallow Water Placement Pilot Project (Project), located in South San Francisco Bay, Alameda County, California. The U.S. Army Corps of Engineers (Corps) proposes to modify the proposed action and requests a written concurrence that the Corps’ proposed Project 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. On July 5, 2022, the U.S. District Court for the Northern District of California issued an order vacating the 2019 regulations that were revised or added to 50 CFR part 402 in 2019 (“2019 Regulations,” see 84 FR 44976, August 27, 2019) without making a finding on the merits. On September 21, 2022, the U.S. Court of Appeals for the Ninth Circuit granted a temporary stay of the district court’s July 5 order. On November 14, 2022, the Northern District of California issued an order granting the government’s request for voluntary remand without vacating the 2019 regulations. The District Court issued a slightly amended order two days later on November 16, 2022. As a result, the 2019 regulations remain in effect, and we are applying the 2019 regulations here. For purposes of this consultation and in an abundance of caution, we considered whether the substantive analysis and conclusions articulated in the letter of concurrence would be any different under the pre-2019 regulations.

We have determined that our analysis and conclusions would not be any different.

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

CONSULTATION HISTORY

By letter dated November 9, 2022, the Corps initiated consultation with NMFS for the Project.

By letter dated February 24, 2023 (NMFS ECO # WCRO-2022-02889; FRN 151422WCR2022SR00209), NMFS concurred with the Corps’ determination that the proposed Project was not likely to adversely affect listed fish or designated critical habitat. The Corps has not initiated the proposed work.

By letter dated September 15, 2023, the Corps requested reinitiation of consultation with NMFS for the Project. The Corps’ request for reinitiation included a supplemental biological assessment of the proposed modifications and potential effects to threatened Central California Coast (CCC) steelhead, threatened green sturgeon and their designated critical habitats. The Corps also provided a supplemental EFH assessment based on modifications to the proposed action.

On September 15, 2023, sufficient information was provided by the Corps, and NMFS confirmed that reinitiation of consultation was required. This concurrence letter replaces the previous concurrence letter, such that the February 24, 2023 concurrence letter is no longer in effect.

PROPOSED ACTION AND ACTION AREA

The Corps is proposing to place dredged material in the waters of South San Francisco Bay, approximately two miles offshore of the Eden Landing Ecological Reserve (Eden Landing). The purpose of the Strategic Placement Pilot Project is to observe and record the ability of tides and currents to move sediment placed in shallow water onto mudflats and marshes in order to increase resilience to rising sea levels. The Project will also compare the economic feasibility of shallow water placement of dredged material to current dredge material placement options in San Francisco Bay. Sediment placement in-water work will occur between June 1 through December

31. The placement area and adjacent mudflat and marsh habitat will be monitored before and after placement.

Dredged material for the proposed Project would be obtained from the Corps’ maintenance dredging program at the Redwood City Harbor (RCH). RCH dredging occurs approximately every two years independent of the proposed Project, and is a covered activity under existing ESA and MSA programmatic consultations. Both the 2011 EFH Consultation for Operations and Maintenance Dredging in the San Francisco Bay Area (June 9, 2011) and the 2015 ESA Section 7 Consultation for the Long-Term Management Strategy (LTMS) for the Placement of Dredged Material in the San Francisco Bay (July 20, 2015) include the Corps’ maintenance dredging activities at the RCH.

https://www.fisheries.noaa.gov/resource/tool-app/environmental-consultation-organizer-eco https://www.fisheries.noaa.gov/resource/tool-app/environmental-consultation-organizer-eco https://eco.fisheries.noaa.gov/suite/sites/eco

This Project involves placing approximately 100,000 cubic yards (cy) of dredged material over approximately 138 acres in shallow water (9-12 feet mean lower low water (MLLW)). The 138-acre area has been divided into placement “cells” of approximately 5 acres each; these areas have been identified as optimal locations to maximize sediment transport towards the nearby mudflats and marshes. Dredged material placement would occur using a scow (i.e., barge) that would be loaded with approximately 900 cy of dredged material for each placement. Sediments would be transported by tug boat to the designated cell where the scow would release the dredged material by opening the bottom doors of the scow. The scow and tug would drift through the cell as material is released. The maximum depth of the sediment layer resulting from placement is expected to be approximately 4-12 inches. Sediment deposition onto the target mudflat and marshes is anticipated to be much less; approximately 0.04 inch of accretion per two-month period following placement.

Approximately 112 scow loads would be needed to place the total 100,000 cy of dredged material. Each scow load would take approximately nine minutes to release, and four to five loads would be released in each placement cell. The release of material would occur during high tide. Two to six scows of material, on average, would be released each day depending on the tidal conditions and transit time from RCH to the placement cell. The scow and tug require minimum water depth of ten feet. Work is proposed to occur between June 1 and December 31, 2023, and is expected to take 19-56 days. At maximum, dredged material placement could occur 24 hours a day.

The placement area and the adjacent mudflat and marsh would be monitored before and after material placement. The pre-project monitoring would include: bathymetry and topography surveys; suspended sediment concentration sampling and wave condition observations; benthic community sampling; sediment flux measurements; and sediment accretion rate measurements in the adjacent Eden Landing marsh. The post-project monitoring would repeat the pre-project surveys for comparison and identification of sediment flux and/or accretion. Sediment transport dynamics would be tracked using tracer particles. Tracer particles consist of non-toxic, dyed, sand or silt particles bound to magnetite (retrievable with magnets). Sediment deposition onto Eden Landing would be conducted using glass filter pads along transects. Vegetation surveys at Eden Landing would also be conducted. To assess the impacts of food availability for benthic consumers, such as fish and water birds, core samples (approximately 0.5 cubic feet each) would be collected to quantify the foraging resources. A Before After Control Impact (BACI) framework would be developed to guide this sampling effort. Pre- and post-placement eelgrass surveys would be conducted and will follow the guidelines provided in the California Eelgrass Mitigation Policy (CEMP; NMFS 2014).

The proposed surveys, assessment of the benthic community and foraging resources, and eelgrass monitoring are described in detail in the draft monitoring plan “Evaluating the benefits and impacts in shallows and marshes of a pilot strategic sediment placement project in San Francisco Bay” provided to NMFS with the Corps’ original consultation request. The final monitoring plan is anticipated to be completed prior to Project implementation.

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

The action area is located in South San Francisco Bay and consists of the dredged material placement site, transit route between the placement site and RCH, and the shallow water habitat where dredged material is expected to disperse and subsequently settle. The placement site is approximately 138 acres, located approximately two miles offshore of Eden Landing in water depths ranging from 9 to 12 feet MLLW. The benthic habitat in the action area consists of soft bottom habitat, and may also include areas of oyster shell deposits and sandy sediment. These benthic habitats are utilized by several species of aquatic invertebrates and bottom dwelling fish (Thompson et. al, 2007). Eelgrass (Zostera spp.) and eelgrass habitat is located in the action area along the Eden Landing shoreline. Recent surveys show a band of eelgrass located approximately one mile offshore. Eelgrass forms dense beds of grass-like shoots that provide year-round fish habitat in soft sediments of the lower intertidal and shallow subtidal areas, providing three-dimensional structure in sandy or muddy soft bottom habitat, adding to fish forage and rearing habitat.

BACKGROUND AND ACTION AGENCY’S EFFECTS DETERMINATION

The Corps determined the proposed Strategic Placement Pilot Project may affect, but is not likely to adversely affect Central California Coast (CCC) steelhead, threatened Southern Distinct Population Segment (DPS) of North American green sturgeon, and their designated critical habitats. The Corp’s finding of not likely to adversely affect listed species and designated critical habitat is based on the timing of proposed activities, relative size of the Project area, and low risk of species occurrence in the Project area.

Available information indicates the following listed species (Distinct Population Segments or DPS) under the jurisdiction of NMFS may be affected by the proposed Project:

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). CCC steelhead pass through the San Francisco Bay Estuary during their downstream migration as smolts to the ocean and during their upstream migration to spawn as adults. Their migrations generally take place in the winter and spring months (Fukushima and Lesh 1998).

The life history of threatened green sturgeon in California is summarized in Adams et al. (2002) and NMFS (2015). The Southern DPS (sDPS) of North American green sturgeon are anadromous, making migrations through the San Francisco Bay estuary to the Sacramento River in the spring, with peaks in April-June (Moyle et al. 1995). Green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River, and as juvenile green sturgeon age, they migrate downstream and live in the lower delta and bays. Green sturgeon juveniles spend three to four years in the estuary, before entering the ocean, and likely optimize their growth opportunities in summer by foraging in the relatively warm estuarine water (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 throughout the San Francisco Bay Estuary year-round. Recent studies recorded peak occurrence for all life stages of green sturgeon in the spring months in Suisun and San Pablo Bays, with few occurrences recorded in South San Francisco Bay (Miller et al. 2020).

Regarding EFH, the Corps has determined that the proposed Project may adversely affect EFH, and these effects are expected to be minor, temporary and localized. The Project area is located within an area identified as EFH for various life stages of fish species managed within the Pacific Coast Salmon Fishery Management Plan (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 FMP and Pacific Coast Salmon FMP. HAPC are described in the regulations as subsets of EFH that are rare, particularly susceptible to human-induced degradation, especially ecologically important, or located in an environmentally stressed area. Designated HAPC are not afforded any additional regulatory protection under MSA, however, federal projects with potential adverse impacts to HAPC are more carefully scrutinized during the consultation process. As defined in the Pacific Groundfish and Salmon FMPs, eelgrass and tidally influenced areas of San Francisco Bay Estuary, including the proposed Project area, are identified as HAPCs.

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 include potential burial of benthic organisms and fish, degradation of water quality from increased turbidity and suspended sediment, and increased sediment deposition in shallow mudflat and marsh areas. The action area does not include freshwater summer and fall juvenile steelhead rearing habitat. CCC steelhead juveniles pass through the San Francisco Bay Estuary during their downstream migration as smolts to the ocean. The proposed in-water work period for this Project avoids the migratory periods of CCC steelhead smolts. Their peak migrations generally take place in the winter and spring months between February and May. Thus, NMFS anticipates CCC steelhead smolts will not be present in the action area during Project activities. As described below, impacts associated with the placement of dredged material are anticipated to fully dissipate prior to the CCC steelhead smolt outmigration period; therefore, any Project-related effects to CCC steelhead smolts are anticipated to be discountable.

The proposed sediment placement within the 138-acre placement area could result in the injury or burial of fish species, however, due to factors described below, adult CCC steelhead and sDPS green sturgeon are expected to avoid injury and burial. Small numbers of adult CCC steelhead and sDPS green sturgeon may be present during sediment placement activities. With shallow water depth at the placement site and the water depth requirements of the scow, adult steelhead and green sturgeon will likely be startled by the maneuvering of the scow into each placement cell and vacate the area prior to the release of sediment. The ability of adult steelhead and green sturgeon to detect noise, turbidity, water velocities and other environmental cues is expected to provide protection as the loaded scows maneuver into shallow water during sediment placement.

Adult steelhead and green sturgeon that react behaviorally would have large areas of adequate habitat in the adjacent areas in South San Francisco Bay to disperse. Additionally, relatively few steelhead and green sturgeon are likely to be within the action area during the short duration of Project activities, and those that may occur would be of sufficient size to possess a relatively strong swimming ability. For these reasons, effects to CCC steelhead or sDPS green sturgeon from the Project’s sediment placement activities are expected to be insignificant.

Degradation of water quality in the form of increased turbidity may also affect CCC steelhead and sDPS green sturgeon. 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 sediment loads remain high for extended periods 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).

Sediment plumes that occur as a result of the placement of sediment by this Project are expected to increase turbidity to concentrations above ambient levels, but the effects of degraded water quality are expected to be temporary and acute, resolving within one tidal cycle or less (Roegner et al. 2021). Furthermore, turbidity measured near the Project area indicates that background turbidity levels are typically high during the June-December time period. Sediment core samples to monitor impacts on food availability for benthic foraging could also result in temporary increases in turbidity and benthic disturbance; however, the area affected will be very small and effects temporary. Other pre- and post-project monitoring activities would not affect water quality or disturb benthic habitat. For these reasons, the potential effects of sediment placement and the associated monitoring program on water quality are expected to be insignificant for CCC steelhead and sDPS green sturgeon.

Following the strategic placement of dredged materials, sediment will transport onto nearby wetlands and mudflats over a period of several months. Consequently, the Project may increase turbidity and suspended sediment levels as materials move. However, due high background levels of turbidity in South San Francisco Bay, Project-related turbidity increases following placement activities are not expected to be measurable, and effects are anticipated to be insignificant for CCC steelhead and sDPS green sturgeon.

The action area is located within designated critical habitat for CCC steelhead sDPS 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 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 sDPS green sturgeon in estuarine areas include food resources, water flow, water quality, migratory corridor, water depth, and sediment quality.

During the dredged material placement and sediment core sampling, critical habitat will be temporarily affected by potential increases in turbidity and disturbance of benthic habitat. As discussed above, water quality effects on listed fish, in the form of increased turbidity, are expected to be temporary and insignificant. Regarding disturbance of the benthic community, the placement of sediment within the 138-acre placement area would result in a temporary layer of 4 to 12 inches of sediment on top of the existing bay floor. Some loss of invertebrate prey items may occur due to burial, and core sampling is expected to remove invertebrate prey items. The loss of benthic invertebrates can reduce the foraging value of the area for listed fish as foraging by green sturgeon typically occurs on tidal flats and shallow subtidal areas (Kelly et al. 2007, Dumbauld et al. 2008), and foraging by juvenile salmonids in estuarine areas typically occurs within the upper portion of the water column or within shallow wetland channels (Dunford 1975, Bottom et al. 2011). Although the placement of sediment and core sampling may remove some invertebrates, the majority of benthic organisms are expected to survive sediment placement. If any benthos are lost during Project implementation, recolonization by macroinvertebrates is expected to occur within a few months due to the relatively thin layer of sediment placement (4- 12 inches) and the small area affected by individual core samples (0.5 cubic feet). Roegner et al.

(2021) found that the impacts of a thin layer of sediment placement were temporary and posed no direct threat to epifauna. For these reasons, NMFS expects that Project activities will not significantly affect PBFs associated with foraging by listed fish in the action area. Based on the above, the potential effects of this Project are considered insignificant and are not expected to result in adverse impacts to CCC steelhead and sDPS green sturgeon designated critical habitats.

Conclusion

Based on this analysis, NMFS concurs with the Corps 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 Corps 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 revised proposed action would adversely affect EFH for various life stages of fish species managed under the Pacific Groundfish FMP and Coastal Pelagic FMP through increased turbidity, loss of benthic forage fish and their prey, and disturbance of benthic habitat. Additionally, NMFS determined that the placement of sediment may adversely affect eelgrass habitat through increased turbidity. Eelgrass is considered a habitat-forming species for the multiple benefits that it provides to the subtidal community. Eelgrass provides foraging and refuge for young fish and invertebrates, traps sediment and stabilizes the substrate, reduces the force of wave energy and subsequent coastal erosion, produces oxygen, filters polluted runoff, absorbs excess nutrients, and increases carbon sequestration. Pre- and post-sediment placement eelgrass surveys will be conducted, as described in the CEMP (NMFS, 2014), and mitigation for impacts to eelgrass would occur if indicated by survey results.

The proposed sediment placement could also result in the burial of fish and invertebrates and adversely affect EFH as the Project would result in a temporary layer of 4 to 12 inches of sediment on top of the existing bay floor. The Corps has proposed to conduct core sampling of the benthic habitat that will provide information regarding the existing and affected fish forage habitat in the Project area. The proposed Project includes avoidance and minimization measures and sampling and monitoring of Project impacts on fish forage habitat. Thus, NMFS has no practical EFH Conservation Recommendations to provide.

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)). This concludes the MSA consultation.

Please direct questions regarding this letter to Sara Azat, North Central Coast Office in Santa Rosa, California at (707) 575-6067 or sara.azat@noaa.gov.

Sincerely, Brian Meux Acting San Francisco Bay Branch Supervisor North-Central Coast Office cc: Dr. Elizabeth Campbell, Corps of Engineers (elizabeth.a.campbell@usace.army.mil) Julie Beagle, Corps of Engineers (julie.r.beagle@usace.army.mil) Copy to E-File FRN 151422WCR2023SR00204

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