Final_1122_Environmental Compliance.pdf

San Francisco Bay Strategic Shallow-Water Placement Pilot Project

Appendices

18 April 2023 U S A rmy Co r p s of Enginee rs Sa n F rancisco District

Emeryville Crescent Marsh: Photo by Michael Layefsky

Whale’s Tail Marsh: Photo by Cris Benton, Professor of Architecture, UC Berkeley (retired)

TABLE OF CONTENTS

Appendix A – ENVIRONMENTAL COMPLIANCE

1. Summary of compliance with applicable laws and regulations

2. Endangered Species Act (ESA) and Magnuson-Stevens Fishery Conservation and

Management Act

3. Clean Water Act

4. Clean Air Act and Climate Change (Green House Gases)

5. Coastal Zone Management Act: CONSISTENCY DETERMINATION

6. Fish and Wildlife Coordination Act (FWCA) Planning Aid Letter

7. National Historic Preservation Act

Appendix B – PLAN FORMULATION

Appendix C – HYDRAULIC AND SEDIMENT MODELING REPORT

Appendix D – MONITORING PLAN

Appendix E – REAL ESTATE PLAN

Appendix F – CEQA CHECKLIST

Appendix G – PREPARERS

Appendix H – AGENCY AND PUBLIC PARTICIPATION

For further information regarding this document, contact:

Julie Beagle Julie.R.Beagle@usace.army.mil

(415) 503-6780

Arye Janoff Arye.M.Janoff@usace.army.mil

(415) 503-6846

U.S. Army Corps of Engineers, SF District Environmental Services Branch 450 Golden Gate Avenue 4th Floor San Francisco, CA 94102

A p pendix A – ENVIRONMENTAL COMPLIANCE

1. SUMMARY OF COMPLIANCE WITH APPLICABLE LAWS AND REGULATIONS

1 F E D E RA L LA W S

CLEAN AIR ACT

Clean Air Act, 42 U.S.C. § 1857h-7, et seq. No general conformity analysis is needed because the action alternatives are below de minimus thresholds. The proposed action would not exceed national ambient air quality standards based on modeled estimates of emission rates during project implementation. Modeled estimates of emission rates during project implementation demonstrate that the proposed action would not exceed applicability rates (Appendix A(4)).

CLEAN WATER ACT

Clean Water Act, 33 U.S.C. § 1251, et seq. The proposed action would involve discharge of fill material into Waters of the U.S. in the lower South Bay. Although USACE does not issue permits for their own projects, USACE does comply with the guidelines and substantive requirements of Section 404, including Sections 404(b)(1) and 401. A Section 404(b)(1) analysis was conducted on the recommended plan (Appendix A(3)). The analysis concluded that the placement of approximately 100,000 CY would not result in impacts to waters of the U.S. or wetlands. Initial coordination with the RWQCB was conducted and the RWQCB has indicated its support for the project and acknowledges the future requirement to obtain a Section 401 water quality certification prior to initiation of the work. The dredging contractor will be required to implement the measures listed in the BMPs and to avoid and minimize adverse effects on water quality. The project is in full compliance with the CWA as a Section 401 water quality certification was obtained on 1 February 2023.

COASTAL ZONE MANAGEMENT ACT

Coastal Zone Management Act, 16 U.S.C. § 1456, et seq. Under Section 307 of the CZMA, the San Francisco Bay Conservation and Development Commission (BCDC) (I.e., not the California Coastal Commission (CCC)), has jurisdiction over federal activities in San Francisco Bay to ensure they are “consistent to the maximum extent practicable” with the “enforceable policies” of BCDC’s NOAA-approved San Francisco Bay segment (I.e., the San Francisco Bay Plan) of the California coastal management program (CCMP; 15 CFR § 923, Subpart K; https://bcdc.ca.gov/bcdc-jurisdiction-authority.html). A Consistency Determination has been prepared and was submitted to BCDC on 12 December 2022, and 20 January 2023 (Appendix A(5); see California Coastal Act, below). The project is in full compliance with the CZMA after obtaining a Letter of Agreement from BCDC on 14 April 2023 concurring with the Consistency Determination.

https://bcdc.ca.gov/bcdc-jurisdiction-authority.html

ENDANGERED SPECIES ACT

Endangered Species Act of 1973, ; 16 U.S.C. § 1531, et seq. Based on the locations of the proposed work, the listed species that could be affected by the proposed action include the California Least Tern, Ridgway’s rail, Western snowy plover, and Southern salt marsh harvest mouse under the jurisdiction of USFWS; and the southern DPS of North American green sturgeon Southern DPS, Central California Coast DPS of steelhead, and the critical habitats of these two species ,under the jurisdiction of NMFS. The USACE has determined that the project will not affect FESA-listed species under the jurisdiction of the USFWS, and determined that the project may affect, but is not likely to adversely affect the FESA-listed species and critical habitats under the jurisdiction of NMFS. The USACE submitted a request for concurrence with a not likely to adversely affect determination to NMFS (Appendix A(2)) on 9 November 2022. The project is in full compliance with FESA as USACE received written confirmation of concurrence from NMFS on 20 February 2023.

FISH AND WILDLIFE COORDINATION ACT

Fish and Wildlife Coordination Act of 1958; 16 U.S.C. § 661, et seq The USFWS is the Federal agency responsible for administering this act, which requires Federal agencies to coordinate with USFWS and State wildlife agencies during the planning of projects that would result in the control or modification of a natural stream or body of water. The FWCA intends that wildlife conservation be given equal consideration with other features of these projects. USACE initiated coordination with USFWS early in the planning process, and USFWS provided a Planning Aid Letter (Appendix A(6)) for full compliance on 18 October 2022, which was finalized on 20 February 2023.

MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

Magnuson-Stevens Fishery Conservation and Management Act of 1996; 16 U.S.C. § 1801, et seq. The Magnuson-Stevens Act establishes a management system for national marine and estuarine fishery resources. This legislation requires that all Federal agencies consult with NMFS regarding all actions or proposed actions permitted, funded, or undertaken that may adversely affect Essential Fish Habitat (EFH). Under the Magnuson-Stevens Act, effects on habitat managed under the Pacific Salmon Fishery Management Plan must also be considered. The USACE incorporated an EFH effects analysis into the NMFS FESA concurrence request and requested consultation under the Magnuson-Stevens Act, in parallel with the Section 7 ESA informal consultation (Appendix A(2)). The project is in full compliance with the Magnuson-Stevens Act as NMFS provided EFH conservation recommendations and USACE responded with a description of proposed measures for avoiding, minimizing, mitigating, or otherwise offsetting the impact of the activity on EFH, completing the consultation with a letter of concurrence on 20 February 2023.

MIGRATORY BIRD TREATY ACT

Migratory Bird Treaty Act of 1928, 16 U.S.C. § 715, et seq. USFWS is the Federal agency responsible for administering this act, which implements a treaty between the U.S. and Great Britain (for Canada), Mexico, Japan, and the Soviet Union (now Russia) for the protection of migratory birds. Unless permitted by regulations, this law prohibits anyone to "pursue, hunt, take, capture, kill, attempt to take, capture or kill … any migratory bird …or any part, nest, or egg of any such bird" (16 U.S.C. § 703). Areas in the study area have foraging, resting, nesting, and breeding habitat for numerous migratory birds. The project is not expected to affect any migratory bird species or habitats because dredge placement activities will occur 2 miles offshore and abundant alternative foraging habitat in San Francisco Bay is available, and project sedimentation rates in wetland resting, nesting, and breeding habitats will be so low they will be difficult to measure.

MARINE MAMMAL PROTECTION ACT

The Marine Mammal Protection Act (16 U.S.C. §§ 1361-1421h), adopted in 1972. The MMPA makes it unlawful to take or import any marine mammals and/or their products.

Under Section 101(a)(5)(D) of this act, an incidental harassment permit may be issued for activities other than commercial fishing that may impact small numbers of marine mammals. An incidental harassment permit covers activities that extend for periods of not more than 1 year, and that will have a negligible impact on the impacted species.

Amendments to this act in 1994 statutorily defined two levels of harassment. Level A harassment is defined as any act of pursuit, torment, or annoyance that has the potential to injure a marine mammal in the wild. Level B harassment is defined as harassment having potential to disturb marine mammals by causing disruption of behavioral patterns including, but not limited to, migration, breathing, nursing, breeding, feeding, or sheltering.

The project alternatives are not expected to result in impacts to marine mammals that would require an incidental harassment permit.

NATIONAL ENVIRONMENTAL POLICY ACT

National Environmental Policy Act of 1969; 42 U.S.C. § 4321, et seq. The Council on Environmental Quality (CEQ) is responsible for ensuring that Federal agencies operate in accordance with NEPA, which requires full disclosure of the environmental effects, alternatives, potential mitigation, and environmental compliance procedures of most Federal management, regulation, or funding activities that affect the environment. NEPA requires the preparation of an environmental document to ensure that Federal agencies accomplish the law’s purposes. Full compliance with NEPA will be achieved when the FONSI is signed.

NATIONAL HISTORIC PRESERVATION ACT

National Historic Preservation Act of 1966; 54 U.S.C. § 300101, et seq. The SHPO in each state is responsible for ensuring that Federal agencies comply with Section 106 of this act, which requires that they consider the effects of a proposed undertaking on properties that have been determined to be eligible for, or included in, the National Register of Historic Places. The Section 106 review process consists of four steps: (1) identification and evaluation of historic properties; (2) assessments of the effects of the undertaking on historic properties; (3) consultation with the SHPO and appropriate agencies to develop a plan to address the treatment of historic properties; and (4) concurrence from the SHPO regarding the agreement or results of consultation. A description of SHPO and tribal consultation activities is included in Appendix A(7)). The project is in full compliance with the NHPA after obtaining concurrence from SHPO on the Section 106 analysis on 22 December 2022.

SUBMERGED LANDS ACT

The Submerged Lands Act of 1953 (43 U.S.C. § 1301 et seq.) grants states title to all submerged navigable lands within their boundaries. This includes navigable waterways, such as rivers, as well as marine waters within the state’s boundaries, generally three geographical miles from the coastline. Section 1311(d) of the Submerged Lands Act provides that nothing in the act shall affect the use, development, improvement, or control by or under the constitutional authority of the United States for the purposes of navigation or be construed as the release or relinquishment of any rights of the United States arising under the constitutional authority of Congress to regulate or improve navigation. In compliance with this act, the California State Land Commission received a copy of this Environmental Assessment and had the opportunity to comment on its potential impacts to submerged lands.

ABANDONED SHIPWRECK ACT

The Abandoned Shipwreck Act, 43 U.S.C. §§ 2101–2106, is a federal legislative act, but does protect shipwrecks found in state waters. The Abandoned Shipwreck Act also states that the laws of salvage and finds do not apply to abandoned shipwrecks protected by the act. Under the Abandoned Shipwreck Act, the United States asserts title to abandoned shipwrecks in state waters that are either:

• Embedded in state-submerged lands;

• Embedded in the coralline formations protected by a state on submerged lands; or

• Resting on state-submerged lands and are either included in or determined eligible for the NRHP.

The Abandoned Shipwreck Act also has a provision for the simultaneous transfer, by the federal government, of title for those abandoned shipwrecks to the state(s) in whose waters the wrecks are located. As detailed further in this section, because there are no known shipwrecks within the federal navigation channels or existing placement sites, no impacts are expected to result from the project alternatives.

2 E X E C U T I V E O R DER S

EXECUTIVE ORDER 11990: PROTECTION OF WETLANDS

This order (42 Federal Register [FR] 26961, May 25, 1977) requires federal agencies to minimize destruction of wetlands when managing lands, when administering federal programs, or when undertaking construction. Agencies are also required to consider the effects of federal actions on the health and quality of wetlands. The project alternatives are not expected to result in adverse impacts but rather have beneficial impacts on wetlands.

EXECUTIVE ORDER 13112: INVASIVE SPECIES

The purpose of this order is to prevent the introduction of invasive species, and to provide control for the spread of invasive species that have already been introduced. This order states that the federal government “shall, to the extent practicable and permitted by law, not authorize, fund, or carry out actions that it believes are likely to cause or promote the introduction or spread of invasive species in the United States or elsewhere unless, pursuant to guidelines that it has prescribed, the agency has determined and made public its determination that the benefits of such actions clearly outweigh the potential harm caused by invasive species; and that all feasible and prudent measures to minimize risk of harm will be taken in conjunction with the actions.” The project alternatives are not expected to cause the introduction or substantial spread of invasive nonnative plants or wildlife.

3 S TAT E LA W S

CALIFORNIA ENVIRONMENTAL QUALITY ACT

The California Environmental Quality Act (CEQA) (California Public Resources Code §21000-21178) and the CEQA Guidelines (14 California Code of Regulations 15000-15387) are the primary policies that require projects to analyze potential impacts to land use, as well as to analyze the project’s consistency with land use planning policies applicable to the project. This document is intended to fulfill the requirements of CEQA and the CEQA Guidelines.

PUBLIC TRUST DOCTRINE (CALIFORNIA STATE LANDS COMMISSION)

The California State Lands Commission (CSLC) manages lands in California according to the Public Trust Doctrine. Several of the guiding principles of the Public Trust are:

I. Lands under the ocean and under navigable streams are owned by the public and held in trust for the people by government. These are referred to as public trust lands and include filled lands formerly under water. Public trust lands cannot be bought and sold like other state-owned lands. Only in rare cases may the public trust be terminated, and only where consistent with the purposes and needs of the trust.

II. Uses of trust lands, whether granted to a local agency or administered by the state directly, are generally limited to those that are water dependent or related, and include commerce, fisheries, and navigation, environmental preservation and recreation. Public trust uses include, among others, ports, marinas, docks and wharves, buoys, hunting, commercial and sport fishing, bathing, swimming, and boating. Public trust lands may also be kept in their natural state for habitat, wildlife refuges, scientific study, or open space.

Ancillary or incidental uses are also permitted—that is, uses that directly promote trust uses; are directly supportive and necessary for trust uses; or that accommodate the public’s enjoyment of trust lands. Although trust lands cannot generally be alienated from public ownership, uses of trust lands can be carried out by public or private entities by lease from the CSLC or a local agency grantee.

III. Because public trust lands are held in trust for all citizens of California, they must be used to serve statewide, as opposed to purely local, public purposes (CSLC, 2010).

CALIFORNIA COASTAL ACT

The California Coastal Act includes specific policies (Division 20 of the California Public Resources Code) for planning and regulatory decisions made by the CCC and local governments. The CCC developed the CCMP, pursuant to the requirements of the CZMA, described above. The BCDC, further described below, is the state’s coastal zone management agency responsible for reviewing consistency determinations under the CZMA in San Francisco Bay and developed the San Francisco Bay segment of the CCMP, the San Francisco Bay Plan. For activities outside of the Golden Gate, consistency determinations are reviewed by the CCC.

Article 4 of the California Coastal Act requires that marine resources be maintained, enhanced, and where feasible, restored. The act also requires that special protection be given to areas and species of special biological or economic significance. It further requires that uses of marine environments be such that habitat function, biological productivity, healthy species populations, and fishing and recreational interests of coastal waters are maintained for long-term commercial, recreational, scientific, and educational purposes;

and that marine resources are protected against the spillage of crude oil, gas, petroleum products, and hazardous substances.

MCATEER-PETRIS ACT

The McAteer-Petris Act (California Government Code Section 66000, et seq.), first enacted in 1965, created the BCDC to prepare a plan to protect the San Francisco Bay and shoreline, and provide for appropriate development and public access. This act directs BCDC to exercise its authority to issue or deny permit applications for placing fill; dredging;

or changing the use of any land, water, or structure in the area of its jurisdiction. The BCDC also reviews determinations of consistency with the CZMA for federally sponsored projects.

The San Francisco Bay Plan (Bay Plan) is BCDC’s policy document specifying goals, objectives, and policies for BCDC jurisdictional areas. Pursuant to the federal CZMA, USACE is required to be consistent to the maximum extent practicable with the enforceable policies of the Bay Plan.

SAN FRANCISCO BAY CONSERVATION AND DEVELOPMENT COMMISSION SAN FRANCISCO BAY PLAN

BCDC has permit authority over development of San Francisco Bay and the shoreline pursuant to the McAteer-Petris Act (California Government Code Section 66000 et seq.).

The act requires BCDC to prepare a “comprehensive and enforceable plan for the conservation of the water of San Francisco Bay and the development of its shoreline.”

BCDC’s jurisdiction includes all tidal areas of San Francisco Bay up to the line of mean high tide; all areas formerly subject to tidal action that have been filled since September 17, 1965; and the “shoreline band,” which extends 100 feet inland from and parallel to the San Francisco Bay shoreline.

The Bay Plan, first adopted in 1969, and last updated in 2011, is BCDC’s policy document specifying goals, objectives, and policies for BCDC jurisdictional areas (BCDC, 2007). Policies in the Bay Plan applicable to the proposed project include those in the following categories: Dredging; Fish, Other Aquatic Organisms, and Wildlife; Water Quality;

Tidal Marshes and Tidal Flats; Subtidal Areas; and Navigational Safety and Oil Spill Prevention.

DREDGING POLICIES IN THE BAY PLAN RELEVANT TO THE PROPOSED PROJECT ARE SUMMARIZED BELOW:

Dredging Policy 1. Dredging and dredged material disposal should be conducted in an environmentally and economically sound manner. Dredgers should reduce disposal in San Francisco Bay and certain waterways over time to achieve the Long-Term Management Strategy (LTMS) goal of limiting in-Bay disposal volumes to a maximum of one million CY per year. The LTMS agencies should implement a system of disposal allotments to individual dredgers to achieve this goal only if voluntary efforts are not effective in reaching the LTMS goal. In making its decision regarding disposal allocations, the BCDC should confer with the LTMS agencies and consider the need for the dredging and the dredging projects, environmental impacts, regional economic impacts, efforts by the dredging community to implement and fund alternatives to in-Bay disposal, and other relevant factors.

Dredging Policy 2. Dredging should be authorized when the BCDC can find: (a) the applicant has demonstrated that the dredging is needed to serve a water-oriented use or other important public purpose, such as navigational safety; (b) the materials to be dredged meet the water quality requirements of the Regional Water Board; (c) important fisheries and Bay natural resources would be protected through seasonal restrictions established by the California Department of Fish and Wildlife (CDFW), the United States Fish and Wildlife Service (USFWS), and/or the National Marine Fisheries Service (NMFS), or through other appropriate measures; (d) the siting and design of the project will result in the minimum dredging volume necessary for the project; and (e) the materials would be disposed of in accordance with Policy 3.

Dredging Policy 3. Dredged materials should, if feasible, be reused or disposed outside San Francisco Bay and certain waterways. Except when reused in an approved fill project, dredged material should not be disposed in San Francisco Bay and certain waterways unless disposal outside these areas is infeasible and the BCDC finds: (a) the volume to be disposed is consistent with applicable dredger disposal allocations and disposal site limits adopted by the BCDC by regulation; (b) disposal would be at a site designated by the BCDC;

(c) the quality of the material disposed of is consistent with the advice of the Regional Water Board and the Dredged Material Management Office; and (d) the period of disposal is consistent with the advice of the CDFW, the USFWS, and the NMFS.

Dredging Policy 4. If an applicant proposes to dispose dredged material in tidal areas of San Francisco Bay and certain waterways that exceeds either disposal site limits or any disposal allocation that the BCDC has adopted by regulation, the applicant must demonstrate that the potential for adverse environmental impact is insignificant, and that nontidal and ocean disposal is infeasible because there are no alternative sites available or likely to be available in a reasonable period, or because the cost of disposal at alternate sites is prohibitive. In making its decision whether to authorize such in-Bay disposal, the BCDC should confer with the LTMS agencies and consider the factors listed in Policy 1.

Dredging Policy 5. To ensure adequate capacity for necessary Bay dredging projects and to protect Bay natural resources, acceptable nontidal disposal sites should be secured, and the San Francisco Deep Ocean Disposal Site should be maintained. Furthermore, dredging projects should maximize use of dredged material as a resource consistent with protecting and enhancing Bay natural resources, such as creating, enhancing, or restoring tidal and managed wetlands, creating and maintaining levees and dikes, providing cover and sealing material for sanitary landfills, and filling at approved construction sites.

Dredging Policy 6. Dredged materials disposed in San Francisco Bay and certain waterways should be carefully managed to ensure that the specific location, volumes, physical nature of the material, and timing of disposal do not create navigational hazards;

adversely affect Bay sedimentation, currents, or natural resources; or foreclose the use of the site for projects critical to the economy of the San Francisco Bay Area.

POLICIES IN THE BAY PLAN PERTAINING TO FISH, OTHER AQUATIC ORGANISMS, AND WILDLIFE THAT ARE

RELEVANT TO THE PROPOSED PROJECT ARE SUMMARIZED BELOW:

Fish, Other Aquatic Organisms, and Wildlife Policy 1. To assure the benefits of fish, other aquatic organisms, and wildlife for future generations, to the greatest extent feasible, San Francisco Bay’s tidal marshes, tidal flats, and subtidal habitat should be conserved, restored, and increased.

Fish, Other Aquatic Organisms, and Wildlife Policy 2. Specific habitats that are needed to conserve, increase, or prevent the extinction of any native species, species threatened or endangered, species that the CDFW has determined are candidates for listing as endangered or threatened under the California Endangered Species Act, or any species that provides substantial public benefits, should be protected, whether in San Francisco Bay or behind dikes.

Fish, Other Aquatic Organisms, and Wildlife Policy 4. The BCDC should not authorize projects that would result in the “taking” of any plant, fish, other aquatic organism or wildlife species listed as endangered or threatened pursuant to the state or federal endangered species acts, or the federal Marine Mammal Protection Act, or species that are candidates for listing under the California Endangered Species Act, unless the project applicant has obtained the appropriate “take” authorization from the USFWS, NMFS, or CDFW. The BCDC should give appropriate consideration to the recommendations of the CDFW, NMFS, or USFWS to avoid possible adverse effects of a proposed project on fish, other aquatic organisms, and wildlife habitat.

WATER QUALITY POLICIES IN THE BAY PLAN RELEVANT TO THE PROPOSED PROJECT ARE SUMMARIZED BELOW:

Water Quality Policy 1. Bay water pollution should be prevented to the greatest extent feasible. The Bay’s tidal marshes, tidal flats, and water surface area and volume should be conserved, and whenever possible, restored and increased to protect and improve water quality.

Water Quality Policy 2. Water quality in San Francisco Bay should be maintained at a level that will support and promote the beneficial uses of San Francisco Bay as identified in the Regional Water Board’s Water Quality Control Plan for the San Francisco Bay Basin and should be protected from all harmful or potentially harmful pollutants. The policies, recommendations, decisions, advice, and authority of the State Water Resources Control Board and the Regional Water Board should be the basis for carrying out the BCDC’s water quality responsibilities.

POLICIES IN THE BAY PLAN PERTAINING TO TIDAL MARSHES AND TIDAL FLATS RELEVANT TO THE PROPOSED

PROJECT ARE SUMMARIZED BELOW:

Tidal Marshes and Tidal Flats Policy 1. Tidal marshes and tidal flats should be conserved to the fullest possible extent. Filling, diking, and dredging projects that would substantially harm tidal marshes or tidal flats should be allowed only for purposes that provide substantial public benefits, and only if there is no feasible alternative.

Tidal Marshes and Tidal Flats Policy 2. Any proposed fill, diking, or dredging project should be thoroughly evaluated to determine the effect of the project on tidal marshes and tidal flats and designed to minimize—and if feasible—avoid any harmful effects (Federal Navigation Channels EA/EIR 3.0 Affected Environment and Environmental Consequences).

POLICIES FOR SUBTIDAL AREAS IN THE BAY PLAN THAT ARE RELEVANT TO THE PROPOSED PROJECT ARE

SUMMARIZED BELOW:

Subtidal Areas Policy 1. Any proposed filling or dredging project in a subtidal area should be thoroughly evaluated to determine the local and Bay-wide effects of the project on: (a) the possible introduction or spread of invasive species; (b) tidal hydrology and sediment movement; (c) fish, other aquatic organisms, and wildlife; (d) aquatic plants; and

(e) San Francisco Bay’s bathymetry. Projects in subtidal areas should be designed to minimize—and if feasible—avoid any harmful effects.

Subtidal Areas Policy 2. Subtidal areas that are scarce in San Francisco Bay or have an abundance and diversity of fish, other aquatic organisms, and wildlife (e.g., eelgrass beds, sandy deep water, underwater pinnacles) should be conserved. Filling, changes in use; and dredging projects in these areas should therefore be allowed only if: (a) there is no feasible alternative; and (b) the project provides substantial public benefits.

NAVIGATIONAL SAFETY AND OIL SPILL PREVENTION POLICIES IN THE BAY PLAN RELEVANT TO THE PROPOSED

PROJECT ARE SUMMARIZED BELOW:

Navigational Safety and Oil Spill Prevention Policy 1. Physical obstructions to safe navigation, as identified by the U.S. Coast Guard and the Harbor Safety Committee of the San Francisco Bay Region, should be removed to the maximum extent feasible when their removal would contribute to navigational safety, and would not create significant adverse environmental impacts. Removal of obstructions should ensure that any detriments arising from a significant alteration of Bay habitats are clearly outweighed by the public and environmental benefits of reducing the risk to human safety; or the risk of spills of hazardous materials, such as oil.

Navigational Safety and Oil Spill Prevention Policy 3. To ensure navigational safety and help prevent accidents that could spill hazardous materials, such as oil, the BCDC should encourage major marine facility owners and operators, USACE and the National Oceanic and Atmospheric Administration to conduct frequent, up-to-date surveys of major shipping channels, turning basins, and berths used by deep-draft vessels and oil barges. Additionally, the frequent, up to-date surveys should be quickly provided to the U.S. Coast Guard Vessel Traffic Service San Francisco, masters, and pilots.

2. ENDANGERED SPECIES ACT (ESA) AND MAGNUSON-STEVENS FISHERY CONSERVATION AND

MANAGEMENT ACT

DEPARTMENT OF THE ARMY

SAN FRANCISCO DISTRICT, US ARMY CORPS OF ENGINEERS

450 GOLDEN GATE AVENUE, 4th FLOOR

SAN FRANCISCO, CA 94102-3406

March 22, 2023

Subject: 2023 San Francisco Bay Strategic Shallow-Water Placement Pilot Project – Response to NMFS’s EFH Conservation Recommendation

Dr. Scott Rumsey Acting Regional Administrator Attn: Gary Stern San Francisco Bay Branch Chief 777 Sonoma Avenue, Room 325 Santa Rosa, California 95404

Dear Dr. Rumsey:

On November 9, 2022, the U.S. Army Corps of Engineers, San Francisco District (USACE) requested concurrence from the National Marine Fisheries Service (NMFS) with our determination that the proposed 2023 Dredge Sediment Strategic Placement Pilot project is not likely to adversely affect the Central California Coast (CCC) distinct population segment (DPS) of steelhead (Oncorhynchus mykiss; threatened) and southern DPS of North American green sturgeon (Acipenser medirostris; threatened), or their respective designated critical habitats.

We also requested consultation on Essential Fish Habitat (EFH) pursuant to the Magnuson- Stevens Fisheries Conservation and Management Act (Magnuson-Stevens Act; 50 C.F.R 600.920(e)) and determined that the proposed action may affect EFH managed as part of the Pacific Groundfish Fishery Management Plan (FMP), Pacific Salmon FMP, and Pacific Coastal Pelagic Species FMP.

On February 24, 2023, NMFS concurred with USACE’s determinations and provided the following EFH Conservation Recommendation:

“NMFS recommends that fish surveys be conducted before and after sediment placement in order to identify the impacts of sediment burial to benthic dwelling fish species and their prey.”

This letter provides the response required by section 305(b)(4)(B) of the Magnuson-Stevens Act and below includes a description of measures proposed by USACE for avoiding, minimizing, mitigating, or otherwise offsetting the impact of the activity on EFH.

The proposed project is expected to deposit dredged sediment in a 138-acre area (i.e.,

0.22 square miles) of south San Francisco Bay, whereas the area of Suisun, San Pablo, and San Francisco bays combined is estimated to be about 225 square miles (i.e., assuming dimensions of 75 miles long x 3 miles wide on average). This activity will occur during the period from June 1 through November 30, 2023 and require a maximum of 56 days to complete. Therefore, the dredge material placement area is extremely small relative to the amount of EFH available, and overall project effects to EFH are expected to be minor, temporary, and localized. Additionally,

- 2 -the project purpose is to investigate the ability of tides and currents to move dredge sediment onto existing mudflats and marshes to increase resilience to rising sea levels, which would beneficially affect EFH.A

The USACE has decided not to conduct fish surveys which would be limited in scope due to budget constraints for this project. Such a study would be unable to provide definitive information about project effects on fish behavior, distribution, etc. We will monitor various elements of fish habitat (e.g., benthic prey resources) to provide insight into project effects on EFH. If you would like to further discuss this response, please contact Dr. Beth Campbell of my staff at elizabeth.a.campbell@usace.army.mil, or at (415) 503-6845.

Sincerely, Julie Beagle Environmental Planning Section Chief U.S. Army Corps of Engineers San Francisco District

BEAGLE.JULIE.RU

BEN.1598717792

Digitally signed by

BEAGLE.JULIE.RUBEN.159871779

Date: 2023.03.22 10:43:45 -07'00'

Dr. Tessa Beach Environmental Branch Chief US Almy Corps of Engineers San Francisco District 450 Golden Gate Avenue

Febmary 24, 2023

San Francisco, California 94102-3404

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVJCE

West Coast Region 777 Sonoma Avenue, Room 325 Santa Rosa, California 95404-4731

Refer to NMFS No: WCRO-2022-02889

Re: Endangered Species Act Section 7(a)(2) ConcuITence Letter and Magnuson-Stevens Fishery Conse1vation and Management Act Essential Fish Habitat Response for the 2023 San Francisco Bay Strategic Shallow-Water Placement Pilot Project

Dear Dr. Beach:

On November 9, 2022, NOAA's National Marine Fishe1ies Se1vice (NMFS) received your request for a written concuITence that U.S. Almy Corps of Engineers' (Corps) proposed 2023 San Francisco Bay Strategic Shallow-Water Placement Pilot Project (Strategic Placement Pilot 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 Comt for the Northern District of California issued an order vacating the 2019 regulations that were revised or added to 50 CFR pa1t 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 comt's July 5 order. On November 14, 2022, the No1thern District of California issued an order granting the government's request for volunta1y remand without vacating the 2019 regulations. The Distiict Comt 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 a1ticulated in the letter of concuITence would be any different under the pre-2019 regulations.

We have dete1mined 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 Conse1vation and Management Act (MSA) (I 6 U.S.C. l 855(b )) for this action. NMFS has provided EFH conse1vation recommendations below.

This letter unde1went pre-dissemination review using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act

From: Campbell, Elizabeth A CIV USARMY CESPN (USA) <Elizabeth.A.Campbell@usace.army.mil> Sent: Thursday, December 8, 2022 12:26 PM To: Sara Azat ‐ NOAA Federal <sara.azat@noaa.gov> Cc: Beagle, Julie R CIV USARMY CESPN (USA) <Julie.R.Beagle@usace.army.mil> Subject: RE: [Non‐DoD Source] QUESTIONS ‐ SF Bay Strategic Dredge Placement Pilot

Hi Sara:

Please see our responses below to the questions and comments (in bold) from your November 21, 2022 email. A revised monitoring plan including some of the requested information (e.g., regarding eelgrass) is attached, as is a monitoring schedule.

1. The consultation request letter specifies that the proposed pilot project is not likely to adversely affect the Central California Coast (CCC) distinct population segment (DPS) of steelhead (Oncorhynchus mykiss;

threatened) and southern DPS of North American green sturgeon (5; threatened), or the designated critical habitat of the southern DPS of North American green sturgeon. The proposed project also occurs within CCC steelhead critical habitat; please confirm the Corps' determination.

We apologize for the oversight. Designated critical habitat for CCC steelhead occurs throughout San Francisco Bay and extends landward to the extreme high tide line (50 CFR Part 226). The proposed project would involve placing approximately 100 kcy of dredged material in a shallow water area located about 2 miles offshore from Eden Landing (Whale’s Tail) in south San Francisco Bay, and then allowing natural hydrodynamic processes to transport the sediment onto mudflat and marsh (i.e., strategic placement). The amount of habitat that would be affected is very small compared to the overall amount of bay and estuarine habitat available. Specifically, the placement site will cover about 138 acres or 0.22 square miles compared to the total area of Suisun, San Pablo, and San Francisco bays which is estimated to be about 225 square miles (i.e., assuming dimensions of 75 miles long x 3 miles wide on average). Turbidity is expected to temporarily increase at the placement site, but this would not occur when steelhead are likely to be present due to the June 1 – November 30 placement work window. Benthic fish and invertebrates could be buried and killed by placement activities, but these organisms typically are not consumed by salmonids; effects to steelhead food supply are expected to be insignificant.

Marsh and mudflat habitats may experience increased rates of sediment deposition over several months, which is the intent of the project and expected to benefit steelhead through increased food production and maintenance of rearing habitat complexity. Overall, project effects to steelhead habitat are expected to be minor, temporary, and localized. The USACE has determined that the proposed project is not likely to adversely affect the designated critical habitat of CCC steelhead.

2. One of the stated purposes of the proposed project is to compare the costs of successfully moving dredged sediment to shallow‐water placement areas with the costs of traditional placement (i.e., ocean, in‐water, or confined upland disposal). Will the comparison be strictly fiscal or will the cost to habitat also be considered?

For confined upland disposal, is this assuming the current placement availability only?

While a hypothesis is that shallow‐water placement may wind up being a lower cost option to supporting marsh and mudflat resilience over time, this study will not be able to actively test that notion in the detail you suggest.

Since this is a fully federally funded project, the study funds will be spent to address the incremental cost above the federal standard on the redwood city dredging action in FY23, and monitor the impacts to the benthic habitat and to water quality, and monitor the transport and deposition of sediment post placement. The purpose of the monitoring plan is to understand the impacts to the benthic and pelagic communities (see attached complete/detailed monitoring plan), and to evaluate the impacts and benefits of the project over the period of monitoring.

Strategic shallow water placement may be one of many tools to beneficially use dredged material. This would be in addition to direct (upland) placement at both current sites (Montezuma and Cullinan), and also at other sites as they come online in the future, as well as other methods which have not yet been tested widely in SF Bay such as marsh spraying, thin layer placement, water column seeding and perhaps others. All tools to reuse sediment will be needed given the pace and extent of sea level rise and the projected impacts to the Baylands.

Different methods for reusing material will be appropriate in different settings, and that may change over time.

For example, in a subsided polder such as Cullinan, direct placement is the most appropriate option. That is true for Bel Marin Keys, as it was for Hamilton, Sears Point and other formerly diked Baylands as they get restored and need a large amount of elevation lift before they are breached.

For existing marshes that are eroding or drowning, direct placement would smother marsh vegetation, and compromise topographic complexity. A more appropriate tool for helping existing marshes and mudflats maintain elevation given lack of sediment supply and rising sea levels may be to augment local sediment supply using strategies such as shallow water placement. This pilot project is intended to start to understand the range of options that exist for existing marshes and mudflats that need sediment augmentation.

3. Figure 1 in the consultation request letter shows placement cells in shallow water approximately two miles offshore of the Eden Landing marsh. What is the size (acreage) of the individual blue and yellow cells?

Total is 138 acres of placement area. Each cell will receive a certain number of placements based on the color of the cells. The cells are 500 ft by 500 ft. Each scow will place 900 CY at a time, and then travel back to the dredging area‐ this will occur a total of 112 times across a 2‐month cycle. One or two placements will occur each high tide, spaced approximately 1.5 hours apart if placed on the same high tide. See figure 1 below attached, which hopefully clarifies placement area.

4. Thank you for providing the Draft Monitoring Plan. Do you know when the monitoring plan will be finalized?

We expect to finalize the monitoring plan concurrent with the EA/IS/MND (approximately February 2023). We will add in the eelgrass reference sites per 4a below and perform both pre‐ and post‐survey eelgrass surveys (see attached complete/detailed monitoring plan). However, we had not expected to make any other significant changes to the monitoring plan.

There are a few questions, and concerns that may be addressed in a Final Plan. Specifically, my initial concerns are:

a. Please include reference sites for the eelgrass surveys as monitoring (see NMFS California Eelgrass Mitigation Policy and Implementing Guidelines (CEMP), 2014).

Per NMFS’ policy to recommend no net loss of eelgrass habitat function in California (CEMP 2014), the monitoring plan for the Shallow Water Placement Pilot Project will include pre‐ and post‐surveys of eelgrass in the project area. As described in the EA/IS/MND, the Eden Landing site (see Figure 1 below) was chosen over the Emeryville Crescent Marsh site partially because it avoided a large eelgrass bed under the Bay Bridge. Through conversations with Kathy Boyer (March 30, 2022), and Keith Merkel (April 1, 2022), both felt that the eelgrass that has been mapped in the project area (offshore of Eden Landing) has been ephemeral and they did not consider this to be high quality eelgrass habitat. Both local experts hypothesized that this type of treatment (strategic placement) may be beneficial for eelgrass in the long term. USACE has proposed a research effort in partnership other scientists in the SF Bay and the Pacific northwest to better understand the impacts of beneficial use on eelgrass over time.

Figure 1. Map of location of mapped eelgrass clones per BCDC Eelgrass Impact Assessment Tool. Placement site (138 acres) is shown in light blue outline.

Below, Figure 2 shows the modeling results of the proposed action after a 2‐month modeling window.

(Appendix D here: (https://www.spn.usace.army.mil/Missions/Environmental/). Thickness of sediment deposition near the edge of the marsh scarp, and near eelgrass mapped is projected to be less than .1‐1 mm in thickness (see blue color ramp on image below).

Figure 2. Deposition thickness post modeling runs showing deposition thickness after placement. 10 cm remains in the placement area post 2 months modeling, and will be monitored post placement. Projected thicknesses on mudflats near mapped eelgrass ranges from .1mm (.01 cm) to approximately 1 cm (10mm).

In terms of choosing a reference site, per CEMP guidance, environmental conditions (e.g., sediment, currents, proximity to action area, shoot density, light availability, depth, onshore and watershed influences) at the reference site(s) should be representative of the environmental conditions at the impact area (Fonseca et al.

1998). Where practical, the reference site(s) should be at least the size of the anticipated impact and/or mitigation area to limit the potential for minor changes in a reference site. The nearest site with eelgrass in a similar estuarine environment is near Cogswell Marsh (see northernmost point of eelgrass on Figure 1). This may be the most effective reference site for the Eden Landing Eelgrass surveys but we will confirm with Keith Merkel and Associates in coordination with the USGS and NMFS.

b. Post‐project eelgrass surveys should be conducted, and may need to be conducted for more than one year post‐project (see CEMP).

Per the EA, to verify avoidance of eel grass beds, the PDT or Contractor shall perform preconstruction eelgrass surveys of the Project area during the months of May through September (i.e., the active growth period for eelgrass in San Francisco Bay). All eelgrass surveys shall be performed in accordance with the National Marine Fisheries Service’s (NMFS’s) California Eelgrass Mitigation Policy (October 2014). The pre‐construction survey shall be completed prior to the anticipated start of in‐ or over‐water construction and shall be valid for either 60 days or until the next active growth period if construction occurs after the end of the active growth period.

As stated in the monitoring plan, if the results of the pre‐construction survey indicate that eel grass beds are located where the placement will occur, the Applicant shall prepare and submit to the Water Board a mitigation and monitoring plan that will be implemented to compensate for impacts to eel grass beds, and include post‐ surveys of project area. See attached monitoring plan and schedule. Eelgrass surveys will occur in July 2023 (pre‐ placement), in December 2023 (6 months post‐placement), and in June 2024 (1 year post‐placement).

c. NMFS recommends that fish presence/absence or behavioral monitoring be included in the Draft Monitoring Plan.

We spoke with Levi Lewis and Ali Weber‐Stover through the Wetlands Regional Monitoring Program TAC (which Beth Campbell and Julie Beagle are both members of), and at length on June 10, 2022, about fish monitoring over various substrate types in south San Francisco Bay (I.e., mudflat, shell hash, and bryozoan reefs). They were proponents of doing fish monitoring but given the need for multiple sites including project site and control site, felt that it would be difficult to scale it down to fit a small budget. All parties also recognized that the sampling methodology and questions addressed would be limited. A likely outcome is that zero or a small number of e.g., green sturgeon would be detected but no real information on their behavioral response to dredge material placement. Ultimately, the larger project team (including the Waterboard and BCDC team members) advised us to simplify our biological monitoring to focus on fish habitat through benthic communities (I.e., food supply), water quality, and eelgrass given the limited budget.

The existing monitoring plan has been developed through a partnership with USGS and with input from several parties including members of the WRMP TAC, Keith Merkel, Kathy Boyer, and the USGS PIs and their teams (Karen Thorne, Susan de la Cruz, and Jessie Lacy). The monitoring plan involves a tracer study as well so that the team will be able to track the sediment which otherwise will be too small in deposition thickness to track using traditional survey methods. All told the monitoring plan is over $1 million out of a $3.6 million total project budget, which is more than 27% of the total project budget.

Until we receive this information, we cannot initiate informal ESA and EFH consultations. We are available to help you determine how best to provide this information. If we do not receive a response from you within 30 days, we will discontinue work on your consultation request (and we will close out the request in our tracking system). We will initiate consultation when we receive the needed information (and our tracking system will be updated).

I am particularly interested in discussing the Monitoring Plan for this project. Please let me know if the Corps would like to schedule a time to discuss.

We would be happy to discuss the monitoring plan with you at your convenience. These are times in the next two weeks that work for our schedule, let us know if you have overlapping availability:

Monday December 12: 12‐1pm, 4‐5m Tuesday December 13: 10‐11am Thursday December 15: 9‐10am, 12‐1pm Wednesday December 21: 11am‐12pm

Thanks much Sara for you questions/comments and allowing us to clarify the information.

Beth and Julie

References:

Fonseca, M.S., W.J. Kenworthy, and G.W. Thayer. 1998. Guidelines for the conservation and restoration of seagrasses in the United States and adjacent waters.