National Marine Fisheries Service (NMFS) Letter of Concurrence Alameda Point Outpatient VA Clinic.pdf

April 9, 2021 Refer to NMFS No: WCRO-2021-00707

Glenn M. Elliott Director, Environmental Program Office (003C2) Office of Construction and Facilities Management Department of Veterans Affairs 810 Vermont Avenue, NW Washington, D.C. 20420

Re: Endangered Species Act Section 7(a)(2) Concurrence Letter and Magnuson-Stevens

Fishery Conservation and Management Act Essential Fish Habitat Response for the Alameda Point Multi-Specialty Outpatient Clinic Project in Alameda County, California

Dear Mr. Elliott:

On May 6, 2020, NOAA’s National Marine Fisheries Service (NMFS) received your request for a written concurrence that the Department of Veterans Affairs’ (VA) implementation of the Alameda Point Multi-Specialty Outpatient Clinic Project (Project) is not likely to adversely affect (NLAA) 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 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://eco.fisheries.noaa.gov]. A complete record of this consultation is on file at NMFS North-Central Coast Office, Santa Rosa, California.

Consultation History The VA requested formal consultation with NMFS by letter on May 6, 2020. On June 11, 2020, NMFS requested additional information by email regarding construction details, and NMFS suggested revising the VA’s EFH determination from ‘no effect’ to ‘may adversely affect’.

Construction details requested by NMFS included the following items: cofferdam and dewatering activities; pile driving; volume and location of riprap; use of herbicides for non-native plant control; and the stormwater management system. On July 9, 2020, the VA provided a response by email which addressed some of the above items. On August 14, 2020, NMFS https://eco.fisheries.noaa.gov/suite/sites/eco requested additional information by email regarding construction methods and post-construction effects. On November 2, 2020, the VA responded by email with information regarding construction of the Project’s outfalls. On December 17, 2020, NMFS provided a list of outstanding information needs by email to orient the new VA project manager. On January 7, 2021, NMFS and the VA’s consultant, HDR, Inc., discussed by telephone the consultation process and remaining information needs.

On March 2, 2021, the VA provided a letter to NMFS revising their ESA effects determination and requested concurrence with a finding of ‘not likely to adversely affect’ listed species and designated critical habitat. The March 2, 2021, VA letter also provided a response to a previous NMFS information request. On March 10, 2021, the VA transmitted the Project’s Noxious Weed Control Plan, Stormwater Treatment System Operations and Maintenance Manual, Stormwater Pollution Prevention Plan, information regarding the amount and location of riprap, and additional information regarding cofferdams and dewatering for construction. On a March 18, 2021 conference call, NMFS, the VA, HDR, Inc. and the U.S. Army Corps of Engineers discussed the new Project materials provided to NMFS on March 10, 2021. On March 30, 2021, the VA revised the Project’s EFH effects determination by email from ‘no effect’ to ‘may adversely affect,’ and provided the remaining information requested by NMFS regarding herbicide use, habitat effects clarification, and expected post-construction stormwater quantity and quality. Sufficient information was received on March 30, 2021, for NMFS to initiate consultation.

Proposed Action and Action Area The VA proposes to construct a development within a 112-acre upland area on Alameda Point in the County of Alameda, California. Buildings and structures will consist of a Veterans Health Administration Outpatient Clinic, Veterans Benefits Administration Outreach Office, National Cemetery Administration Columbarium, and Conservation Management Office. The proposed development is located on a portion of the former Naval Air Station Alameda property known as the VA Transfer Parcel. Proposed construction activities that may affect San Francisco Bay (Bay) shoreline and waters consist of installation of new drainage outfalls, a new stormwater management system, and rock riprap shoreline stabilization. In addition to the new VA facilities, the Project proposes to restore 7.4 acres of tidal wetland habitat, approximately 3 acres of transition zone bounding the restored tidal marsh, and enhancement of an existing 13.7-acre muted tidal wetland area. The Project will be completed in four consecutive years, and will include two in-water work periods from June 15 through November 30.

Project activities occurring in upland areas that are not expected to affect Bay waters during construction will include the following: replacement of concrete and asphalt; excavation of trenches for stormwater pipes; drainage pipe installation; and construction of the development (buildings, sidewalks, and parking lots). Excavated materials will be stored at an onsite upland soil disposal area. Once the new drainage pipes and junction boxes are in place, the excavated area will be backfilled. The remaining deteriorated drainage pipes will be abandoned in place in upland areas. In addition, a 24-inch diameter stormwater pipe will be installed for future use by the City of Alameda. The pipe will be capped until this area adjacent to the VA property is built out. It is anticipated that the City of Alameda’s development of this adjacent parcel will require authorization from the Army Corps of Engineers (Corps) and result in a future section 7 consultation between NMFS and the Corps.

To provide permeability, infiltration, treatment, and reduction of stormwater runoff from impervious areas into the Bay and Oakland Inner Harbor (Harbor), the stormwater system will include 70 bioswales and several catch basins adjacent to roads and parking areas. Bioswales are permeable soil-based retention areas designed to remove common stormwater pollutants. The upland area of the project site will be graded to match the existing drainage patterns to the maximum extent possible. Due to the site topography and relative flatness (approximately 0.1% slope) of the upland area, there is no anticipated offsite run-on to this Project’s development. The stormwater system will be sized to completely infiltrate stormwater flows up to a two-year storm. The Project will reduce impervious surfaces by 4.66 acres compared to existing conditions. In addition, the overall permeability of the area is expected to increase as a result of the Project’s installation of bioswales and catch basins. The 10-year stormwater volume is expected to decrease from 57.6 cubic feet per second (cfs) pre-project to 52.4 cfs post-project.

Additional information regarding the Project’s stormwater management system is contained in the following Project documents: Stormwater Treatment System Operations and Maintenance Manual; Stormwater Narratives; and Stormwater Pollution Prevention Plan (SWPPP). The Project is undergoing a 401 Water Quality Certification with the San Francisco Regional Water Quality Control Board (SFRWQCB) in accordance with a Clean Water Act section 404 permit issued by the U.S. Army Corps of Engineers.

Outfalls will be installed in two locations on the north shore of Alameda Point that will discharge into the Harbor, one consisting of a single 36-inch diameter drainage pipe, and the other consisting of two 36-inch diameter drainage pipes. Outfall installation will consist of trenching, installation of flared concrete end sections, and rock riprap shoreline slope stabilization (described below). Outfall construction site isolation from Bay waters will be accomplished by installing a temporary cofferdam at each of the two outfall locations. Cofferdams will be constructed by driving up to 50 steel sheet piles during daylight hours with a vibratory hammer or hydraulic press to a depth of at least 10 feet into the mud substrate. Any existing rock riprap that may impede cofferdam installation will be temporarily removed. To avoid entrapment of fish the following will occur: all cofferdam construction will occur at low tide, fish will be able to volitionally leave the partially constructed cofferdam, and the bayward sheet piles will be installed last when water depths are less than two feet. Cofferdam installation will occur over approximately five days. If seepage through the ground occurs, dewatering will be accomplished by pumping the water to a sediment settling basin or tank before being discharged back to Bay waters. Discharged water will be tested and discharged in accordance with SFRWQCB requirements. The two cofferdams will temporarily occupy a total of 0.035 acres.

New rock riprap will be added to improve the existing rock riprap stabilization structure that exists along the shoreline at the two outfall locations. Rock will be placed surrounding new outfall structures using an excavator working from upland areas. New rock will be matched with the existing size of rock riprap (average three-foot diameter) and existing slope. The total amount of substrate area that will receive new rock fill will be 0.002 acres.

Restoration of the 7.4-acre tidal wetland habitat will involve excavation of the existing ground surface to elevations suitable for the establishment of pickleweed plant (Salicornia spp.). Pilot channels will be excavated to encourage development of a dendritic slough channel network. To provide adequate tidal exchange, an inlet channel will be constructed by removing a portion of existing rock riprap that bounds the southern end of the restored tidal wetland habitat area and lowering the elevation. To minimize tidal scour of the inlet channel, an existing 0.5 acre area of rock riprap (splash pad) will be constructed in the inlet channel that will allow full tidal exchange, and will connect with existing rock riprap at the site. The inlet channel rock area excavation and installation activities will temporarily disturb an additional 0.031 acres of substrate bayward of rock riprap that will be lowered, and will result in additional permanent rock fill of 0.002 acres bayward of the former rock riprap stabilization structure. To minimize the spread of suspended sediment, a turbidity curtain will be deployed to encircle the tidal inlet channel project site for construction of the inlet channel. To avoid fish entrapment, the turbidity curtain will be installed at low tide and installation will begin from shore and be pushed out into Bay waters. The inlet channel construction will occur only at low tide between June 15 and November 30.

The wetland enhancement area is an existing 13.7-acre muted tidal wetland that will remain separated from the 7.4-acre restored tidal wetland area by a levee. The wetland enhancement area is not directly connected to Bay waters, and only receives tidal water through seepage in the existing riprap stabilization structure during higher tide levels. This 13.7-acre site will be enhanced by non-native plant removal by manual, mechanical, and chemical methods (described below) followed by native planting.

A combination of mechanized, hand, and herbicide methods will be used to optimize control non-native invasive vegetation at the restored tidal wetland and muted tidal wetland enhancement area, depending upon the invasive plant species type and location within the site.

Mechanical removal on site is the preferred method, and will be limited to the use of line trimmers and hand tools. Herbicide use is expected to decrease substantially over time, with a low level applied as needed. The herbicide Roundup Custom for Iceplant contains glyphosate, and will be applied in upland and aquatic sites on emerged weeds in fresh or brackish water.

Roundup products will be applied with a surfactant (Magnify). Polaris for Invasive Sea Lavender contains Imazapyr, and will be applied in upland and aquatic areas. Polaris is rainfast in one hour, and application will occur at least two hours before high tide with a surfactant/modified vegetable oil (Competitor). A dye will be used to track herbicide use and minimize overspray.

The specific dye has not yet been selected, and one of the following dyes that have been previously reviewed by NMFS for use in and near aquatic habitat will be selected for use:

Dynamark U.V. Red, Dynamark U.V. Blue, Aquamark Blue, and Hi-Light Blue.

All herbicides shall be applied in accordance with regulations set by the California Department of Pesticide Regulation and according to labeled instruction. Aquatic formulations will not be applied to standing water, and application will be made in such a way as minimize overspray and wind-drift into water (low pressure drift resistant spray nozzles, anti-drift agents, spray shields, and any other means necessary). Herbicide treatments in the restored tidal wetland shall be timed to coincide with the ebb tide and, to the extent feasible, shall be conducted during tidal cycles that maximize the area that will not be inundated within 24 hours of herbicide application. More details on herbicide application are included in the Project document, ‘Noxious Weed Control Plan for Wetland Restoration and Enhancement Project at VA Alameda Point.’

Conservation Measures The measures described below will be implemented during Project activities to avoid and minimize environmental effects:

1. During construction, the Project will treat all of the site stormwater runoff in accordance with the State Water Resources Control Board (SWRCB) Construction General Permit, Order No. 2009-0009-DWQ.

a. To minimize discharge of water with high suspended sediment levels during construction, if water from dewatering activities cannot be contained on site, it would be pumped into suitable detention facilities or Baker tanks or equivalent with sufficient capacity to control the volume of water. Sediment will be allowed to settle out, and remaining water will be tested and discharged in accordance with SFRWQCB requirements.

b. To minimize debris and sediment from entering Bay waters during construction, spoil sites and other debris areas will be located so they do not drain directly into any body of water. Spoil sites will be graded to reduce the potential for erosion.

c. To minimize loose sediment from entering Bay waters during construction, sediment control measures will be implemented in all upland areas where construction occurs within 100 feet of water, including silt fencing, erosion control blankets, check dams, erosion control seeding, or alternate methods where appropriate.

d. Prior to the completion of construction, permanent erosion control will be applied to remaining disturbed soil areas. Additional erosion control best management practices (BMPs) are included in the Project’s draft SWPPP.

e. A spill prevention and control plan will be implemented during construction to minimize chemical spills into Bay waters during construction. Measures will include equipment refueling and maintenance to occur outside of 200 feet from the Bay or Harbor. Spills will be reported to NMFS within 48 hours.

f. Monitoring during construction will be implemented to ensure that erosion and sediment controls are limiting discharge and the site is in compliance with the Construction General Permit. Site inspections will occur before and after rain events. Water quality samples will be collected in association with a significant rain event. More information is included in the Project’s draft SWPPP.

Operations and maintenance To ensure optimal function of the stormwater management system post-construction, inspections and maintenance will be performed on a regular basis to remove sediment from bioswales, catch basins, and outfalls to maintain the hydraulic capacity of the stormwater conveyances and treatment features. For the purposes of stormwater management maintenance and function, it is anticipated that non-chemical controls (i.e., biological, physical, and cultural controls) will be implemented to address any pest problems.

Topography and vegetation monitoring will occur annually post-construction to map and measure habitat conditions in the restored tidal wetland and the tidal wetland enhancement area.

More information on habitat monitoring is included in the Project document, ‘Alameda Point Veterans Affairs Project Final Wetland Mitigation and Monitoring Plan’.

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

Action Area The action area is located on the eastern shore of South San Francisco Bay (Bay), and generally bound by the Oakland Inner Harbor (Harbor) to the north, Bay waters to the west and south, and City of Alameda to the east. This Project’s 112-acre development is a portion of the 624-acre VA-owned and managed VA Transfer Parcel, which is situated on Alameda Point, a peninsula that extends into the Bay in Alameda County, California. The action area includes the 112-acre development area, the northern shoreline of Alameda Point where two stormwater outfalls will be installed, and the southern shoreline on Alameda Point where the tidal wetland restoration and enhancement area will be located. The action area also includes all Harbor and Bay waters within

0.5 mile of the Project components where turbidity and stormwater effects may occur.

The VA Transfer Parcel was the former Alameda Naval Air Station, and the existing site is composed of several large runways, multiple taxiways, and side roads. The unpaved areas of the site are covered with ruderal vegetation and various upland seasonal wetland designated areas.

The Harbor is a navigation channel between the cities of Oakland and Alameda. The Port of Oakland loads commercial cargo vessels on the northern shore of the Harbor. The shoreline and channel have been highly modified for various maritime-related industries including shipbuilding, military functions, shipping, and goods processing. Alameda Point was formerly a shallow mudflat that was filled as early as the late 1800’s. Shoreline areas are dominated by industrial and transportation development including railroad beds, roads, buildings, and parking lots. Various contaminants are transported into the Bay by an assortment of sources such as urban uses, industrial outfalls, municipal wastewater outfalls, municipal stormwater, and legacy pollutants. The substrate at the shoreline is composed of sandy mud, and it is expected that typical benthic invertebrates of San Francisco Bay inhabit the substrate (e.g., worms, bivalves, crustaceans).

Background and Action Agency’s Effects Determination The VA has determined that the Project may affect, but is not likely to adversely affect (NLAA) listed species and their critical habitat. This determination is based on the inclusion of conservation measures and the limited use of the habitat in the action area by listed fish species.

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

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

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 by NMFS (1996; 2016). Central California Coast (CCC) steelhead use the San Francisco Bay primarily as a migration corridor, passing through the Bay on their way to the ocean to rear as juveniles or to upstream areas to spawn as adults.

Adult steelhead typically begin their upstream migrations in early December, and juvenile steelhead migrate downstream through the estuary during the late winter and spring months (Fukushima and Lesh 1998).

The life history of green sturgeon in California is summarized in NMFS (2015; 2018). The Southern DPS (sDPS) of North American green sturgeon spawn in the deep turbulent sections of the upper reaches of the Sacramento River. The sDPS green sturgeon are anadromous, making migrations as adults to the Sacramento River in the spring (Moyle et al. 1995). As juvenile green sturgeon age, they migrate downstream and live in the lower delta and bays of the San Francisco Estuary, spending up to four years there before entering the ocean. Within the San Francisco Estuary, information provided by Kelly et al. (2007) suggests depths less than 10 meters (33 feet) may be preferred during foraging and migration. Adult green sturgeon return from the ocean every few years to spawn, and generally show fidelity to their upper Sacramento River spawning sites. Adult sDPS green sturgeon enter the San Francisco Estuary in late winter through early spring (NMFS 2015) and juvenile, subadult, and adult sDPS green sturgeon may be present in the San Francisco Estuary and in the action area year-round.

Regarding EFH, the VA has determined that the proposed action may adversely affect EFH. The Project area is located within an area identified as EFH for various life stages of fish species managed under the Pacific Coast Groundfish Fishery Management Plan (FMP), the Coastal Pelagic Species FMP, and the Pacific Coast Salmon FMP. San Francisco Estuary, including the Project area, is also designated as an estuary habitat area of particular concern (HAPC) for various federally managed fish species as defined in the Pacific Salmon and Groundfish FMPs.1

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

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.

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.

Effects to Species During construction, the effects of the Project to the above-listed fish are reasonably likely to include elevated underwater sound levels, degraded water quality, and risk of fish entrapment.

Upon completion of construction, the effects of the Project include changes to water quality from the improved stormwater management system. Juvenile and adult CCC steelhead migrate seasonally through South San Francisco Bay, and the Project’s in-water work window (June 15 to November 30) for construction activities avoids the majority of this migration period. CCC steelhead are very unlikely to be present in the action area due to the Project’s location and timing of in-water work. Thus, NMFS anticipates CCC steelhead will not be present in the action area during in-water construction activities. As presented below, impacts associated with in-water construction activities for this Project will be temporary and are expected to fully dissipate when construction activities cease; therefore, any effects to CCC steelhead during in-water construction activities are anticipated to be discountable.

For sDPS green sturgeon during construction, elevated underwater sound levels may co-occur with their presence in the action area during installation and removal of temporary sheet piles for cofferdam construction (June 15 to November 30). Vibratory or hydraulic methods will be used to drive the steel sheet piles. Based on results of hydroacoustic monitoring at various pile driving projects (Caltrans 2020), vibratory and hydraulic methods generate sound levels and sound wave forms that are not expected to cause physical injury or mortality of listed fish. Additionally, the small number of sheet piles (up to 50 sheet piles), installation during dry or shallow water conditions, and short duration of installation (approximately five days), reduces the risk of sturgeon exposure to elevated sound levels. If green sturgeon are present in the action area during the sheet pile installation or removal, elevated levels of underwater sound may startle green sturgeon and result in temporary dispersion from the action area. If green sturgeon were to react behaviorally to the sound produced by construction activities, adequate water depths and area within the adjacent open waters of the Harbor and Bay are expected to provide fish sufficient area to disperse for the duration of sheet pile driving and removal. Therefore, it is anticipated that the effects to sDPS green sturgeon from elevated underwater sound levels produced during construction activities will be insignificant.

Degraded water quality resulting from elevated levels of suspended sediment and potential contaminants (hereafter turbidity) may co-occur with the presence of sDPS green sturgeon due to turbidity during cofferdam installation and removal, dewatering within the cofferdam, silt curtain installation and removal, and temporary stormwater runoff during construction. 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). However, temporary stormwater runoff during construction period is expected to be minimized due to the Project’s proposed erosion and sediment control measures. Cofferdam and silt curtain installation and removal will occur during low tide, minimizing turbidity. The water pumped into the Harbor during cofferdam dewatering is expected to be only water seeping into the cofferdam, and will be pumped through a settling basin before discharge. The removal of the cofferdam and silt curtain will occur after turbidity within the enclosures is allowed to settle, and only small amounts of sediment are expected to suspend. The VA will discharge water into the Harbor pursuant to the National Pollutant Discharge Elimination System Construction General Permit (SWRCB Order No. 2009- 0009-DWQ), and will operate under an approved SWPPP that must sufficiently control, treat, or dilute runoff to meet the standards of the San Francisco Bay Basin Water Quality Control Plan (Basin Plan; SFRWQCB 2015). The Project is designed to comply with these standards, which are expected to limit construction site discharge to levels that are protective of all beneficial uses in the Bay, including listed fish. Based on the above, it is expected that the effects to sDPS green sturgeon from degraded water quality during construction activities will be insignificant.

For sDPS green sturgeon during construction, in the absence of improper silt curtain configuration and deployment and temporary sheet pile cofferdam installation, there would be a risk of inclusion of green sturgeon within the enclosures, exposing fish to elevated levels of turbidity during construction activities. However, this potential effect will be avoided because the silt curtain will be deployed by hand at low tide and installation will start from shore, and be pushed out into Bay waters beginning from the bank and walking it slowly out where depths will be shallow. The silt curtain will have floats on top and weight on bottom that will span the entire water column, preventing fish from entering the work area during several weeks of deployment.

The curtain material will be made from a sturdy fine mesh cloth that will prevent green sturgeon from being caught or trapped by gill or fin. The cofferdam will be installed at low tide and closed when depths are shallower than two feet. Bayward sheet piles will be installed last when water depths are less than two feet to allow fish to volitionally leave the partially constructed cofferdam. These avoidance measures will prevent inclusion of green sturgeon in the silt curtain and sheet pile cofferdam during Project activities.

The Project proposes to apply herbicides to control non-native vegetation, potentially exposing CCC steelhead and sDPS green sturgeon to toxins that may be harmful. However, the Project’s application during low ebbing tides and reduced wind speeds are expected to minimize exposure to fish and the aquatic environment. Herbicides will be applied directly to target plants, and a dye will be used to aid in detecting and preventing drift from the targeted area. The application techniques are expected to give the applicator sufficient control and precision over the spray to prevent overspray, exposure of non-targeted areas, and will reduce the risk of herbicide discharge into tidal waters. If herbicide applications do reach a waterway, they are expected to dissipate or breakdown, depending on multiple abiotic factors. Glyphosate is highly soluble in water. Studies conducted in a forest ecosystem (Feng et al. 1990; Goldsborough et al. 1993;

Newton et al. 1994) found that glyphosate dissipated from streams within 3-14 days. Imazapyr is soluble in water and degrades quickly in the presence of sunlight; therefore, water contamination is generally not a concern (WSDA 2003). One study completed in the state of Washington found that imazapyr was undetectable in the initial tidal exchange following direct application to estuarine sediments (WSDA 2003). Glyphosate and imazapyr are considered relatively non-toxic to fish and do not bioaccumulate in the tissues of aquatic organisms (Gardener and Grue 1996;

Giesy et al. 2000). The adjuvants (Magnify, Competitor) to be used have low toxicity (WSDA 2017). Available dyes (one of the following: Dynamark U.V. Red, Dynamark U.V. Blue, Aquamark Blue, and Hi-Light Blue) will be used in small amounts, and are agriculturally registered food-grade colorants that are highly unlikely to cause toxicity. For these reasons, the potential effects of herbicide application are expected to be insignificant to sDPS green sturgeon and CCC steelhead.

Upon completion of the Project, degraded water quality resulting from ongoing stormwater runoff may co-occur with CCC steelhead and sDPS green sturgeon. If not adequately addressed through management and treatment, long-term stormwater effects to listed species may include the following exposure in the receiving waterbody: flow volume changes; elevated water temperatures; regular contribution of fine sediment; and regular contribution of toxic pollutants.

However, the expected volume of stormwater runoff from the 112-acre area is expected to decrease because permeable surfaces will increase as a result of Project activities, and runoff will be directed to approximately 70 new bioswale areas. The action area is not expected to receive significant off-site run-on due to the location and relatively flat grade of the area surrounding the action area. The Project’s new stormwater management system is designed to divert and treat up to a two-year storm event. Regarding flows that exceed a two-year storm event, the VA will discharge stormwater pursuant to the SFRWQCB 401 Water Quality Certification for this Project, and will operate under a SWPPP and Stormwater Treatment System Operations and Maintenance Manual approved by the SFRWQCB that must sufficiently control, treat, or dilute runoff to meet the standards of the Basin Plan (SFRWQCB 2015). The Project is designed to comply with these standards, and is expected to improve the stormwater quality runoff compared to existing conditions.

Effects to Critical Habitat The action area is located within designated critical habitat for CCC steelhead and sDPS green sturgeon. The physical and biological features (PBFs)2 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. The PBFs of designated critical habitat for green sturgeon in estuarine areas include food resources, water flow, water quality, migratory corridor, water depth, and sediment quality.

During construction, effects to CCC steelhead and sDPS green sturgeon designated critical habitat will include elevated underwater sound levels, degraded water quality, and benthic (bottom) habitat disturbance. Post-construction effects will include changes to stormwater discharges, degraded water quality, altered benthic habitat, and tidal wetland habitat restoration.

2 The designation(s) of critical habitat for these species used the term primary constituent element (PCE) or essential features. The new critical habitat regulations (81 FR 7414) replace these terms 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 PCEs, PBFs, or essential features. We use the term PBF from this point forward in this letter to mean PCE or essential feature, as appropriate for the specific critical habitat.

The Project’s potential effects associated with elevated underwater sound levels, degraded water quality, and changes to stormwater flows on critical habitat are expected to be insignificant for the reasons presented above.

During construction, temporary disturbance will occur over 0.066 acres of intertidal benthic habitat for installation of two new stormwater outfalls (0.035 acres), and construction of the inlet channel to the tidal wetland restoration area (0.031 acres). Post-construction, permanent alteration of 0.004 acres of intertidal benthic habitat will occur from installation of the two new outfalls with rock riprap (0.002 acres), and the tidal wetland restoration rock splash pad (0.002 acres). These Project activities will exclude fish during cofferdam and turbidity curtain deployment, and benthic disturbance and permanent alteration could potentially reduce foraging area for CCC steelhead and sDPS green sturgeon that prey on benthic invertebrates inhabiting the substrate of the action area (e.g., crustaceans, clams). However, disturbed and permanently altered areas during Project activities along the Harbor and Bay shorelines will impact only a small area of severely degraded habitat. The existing shorelines are highly modified and degraded from decades of industrial harbor and military airport use. These highly modified shorelines are unlikely to provide quality habitats for foraging and rearing by any life stage of steelhead and green sturgeon, and the Project is not expected to further degrade conditions.

Substrate disturbed during construction is expected to return to pre-project conditions within a few weeks due to recolonization of benthic invertebrates from adjacent areas. For these reasons, the benthic habitat disturbance and alteration that will result from Project activities during construction is expected to be insignificant to CCC steelhead and sDPS green sturgeon designated critical habitat.

The restored tidal wetland habitat will be created by removing the rock riprap shoreline stabilization structure and excavating the existing upland area down to elevations suitable for the establishment of a pickleweed (Salicornia spp.) dominated tidal marsh. Pilot tidal channels will be excavated, and full tidal exchange will be restored to 7.4 acres that is expected to provide benefits to CCC steelhead and sDPS green sturgeon critical habitat in the action area. It is expected that within several months after tidal connectivity is restored, marsh vegetation and benthic invertebrates will begin recruiting to the newly excavated area. Juvenile steelhead, green sturgeon, and other estuarine fish will have access to the restored area during high tide and may benefit from increased opportunities for foraging and refuge. As the tide recedes, fish will be able to retreat to subtidal areas in adjacent shoreline areas (Levy and Northcote 1982; Hering et

al. 2010). Detrital input from tidal wetland habitat supports invertebrate productivity within the wetland and on adjacent mudflats (Warwick and Price 1975). The productivity of crustaceans, polychaete worms, gastropod and bivalve mollusks, and other potential steelhead and green sturgeon invertebrate prey (Harvey et al. 1977) is expected to increase as a result of restoration.

Based on the above, the restoration of 7.4 acres of tidal wetland habitat is expected to provide benefits to CCC steelhead and sDPS green sturgeon designated critical habitat.

Conclusion Based on this analysis, NMFS concurs with the VA 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 VA 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)).

Based on information provided by the VA and HDR, Inc., proposed construction activities are expected to result in elevated underwater sound levels, degraded water quality, and disturbance to benthic habitat. Post-construction effects may include degraded water quality, a change in stormwater flows, alteration to benthic habitat, and tidal wetland restoration. Therefore, NMFS has determined the proposed action would adversely affect EFH for various life stages of fish species managed under the Pacific Coast Groundfish FMP and the Coastal Pelagic Species FMP.

However, as presented above, short-term effects during construction resulting from elevated underwater sound levels, degraded water quality, and disturbance to benthic substrate are expected to be minimal and localized.

Upon completion of the Project, herbicides will be used to control non-native terrestrial and aquatic vegetation, however effects are expected to be minimal and localized due to the herbicides selected and implementation of conservation measures. Stormwater discharges from upland areas are expected to decrease in quantity and improve in quality due to the overall increase in pervious surfaces and installation of bioswales. Installed rock riprap and outfall structures along the shoreline of Alameda Point will not further degrade the forage and refuge habitat functions of benthic habitat in the Project area. In addition, the tidal wetland habitat restoration area is expected to provide forage and refuge benefits to federally managed fish under the Groundfish and Coastal Pelagic Species FMPs. Therefore, NMFS has no EFH conservation recommendations to provide.

The VA 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 Brian Meux, North-Central Coast Office in Santa Rosa, California at (707) 575-1253, or via email at brian.meux@noaa.gov.

Sincerely, Gary Stern

San Francisco Bay Branch Chief North Central Coastal Office cc: Warren Yip, VA West Region CFM, warren.yip@va.gov

Christine Modovsky, VA West Region CFM, christine.modovsky@va.gov Elizabeth Exter, U.S. Army Corps of Engineers, elizabeth.exter@usace.army.mil Copy to ARN File #151422WCR2020SR00104

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