1122_EA-MND.pdf

Environmental Assessment (with FONSI) and 404 (b)(1) Analysis & Initial Study (with Mitigated Negative Declaration)

San Francisco Bay Strategic Shallow-Water Placement Pilot Project

Emeryville Crescent Marsh: Photo by Michael Layefsky

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

18 April 2023

US Army Corps of Engineers San Francisco District i

TAB LE OF CON TE NT S

1 Proposed Project

1.1 Introduction

1.2 Description and Location

1.2.1 Federal Navigation Projects

1.3 Purpose and Need for Proposed Action

1.4 Basic and Overall Project Purpose

1.4.1 Basic Project Purpose

1.4.2 Overall Project Purpose

1.5 Study Authority

2 Scope of Analysis

2.1 Direct Impacts

2.2 Indirect Impacts

3 Alternatives

3.1 No Action Alternative

3.2 Plan Formulation Summary

3.3 The Final Array of Alternatives

3.4 Modeling

3.5 Proposed Action

3.5.1 Eden Landing Whale’s Tail Marsh (Alternative A: Proposed Action)

3.5.2 Emeryville Crescent Marsh (Alternative B)

3.6 Clean Water Act (404) Alternatives Analysis

4 Effects Analysis

4.1 Existing conditions of analyzed sites

4.1.1 Whale’s Tail Marsh (Alternative A)

4.1.2 Emeryville Crescent Marsh (Alternative B)

4.2 Physical Environment

4.2.1 Water Quality – temperature, salinity patterns and other parameters:

4.2.2 Turbidity, suspended particulates:

4.2.3 Substrate

4.2.4 Currents, circulation, or drainage patterns:

4.2.5 Mixing zone

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4.2.6 Flood Risk Management functions:

4.2.7 Storm, wave, and erosion buffers:

4.2.8 Erosion and accretion patterns:

4.2.9 Air Quality

4.2.10 Climate Change (Greenhouse Gas Emissions)

4.3 Biological Environment

4.3.1 Aquatic habitat and species, including special aquatic sites

4.3.2 Water column habitat

4.3.3 Mudflat, Sandflat, and beach habitat

4.3.4 Marsh habitat

4.3.5 California Least Tern

4.3.6 Ridgway’s rail

4.3.7 Western Snowy Plover

4.3.8 North American Green Sturgeon Southern DPS

4.3.9 Central California Coast Steelhead DPS and Central Valley Steelhead DPS

4.3.10 Longfin Smelt

4.3.11 Salt Marsh Harvest Mouse

4.3.12 Marine Mammals

4.3.13 Habitats of Special Significance

4.4 Human Environment

4.4.1 Cultural Resources

4.4.2 Native American Consultation

4.4.3 Navigation/Transportation

4.4.4 Noise

4.4.5 Recreation (boating, fisheries, other)

4.4.6 Land use classification

4.4.7 Environmental Justice

4.4.8 Conflict with other use plans, policies or controls:

4.4.9 Irreversible changes, irretrievable commitment of resources:

5 Cumulative impacts

5.1 Methodology and Geographic Scope of the Analysis

5.2 Past, present, and Reasonably Foreseeable Future Projects

5.3 Summary of indirect and cumulative effects from the proposed action iii

5.4 Pre- and Post-Project Monitoring

6 Compliance with applicable laws and regulations

7 Agencies Consulted and Public Notification

7.1 Agencies Contacted

7.2 summary and incorporation of comments received during public comment period 124

8 Mitigation Measures

9 Determinations and Statement of Findings

10 References iv

APPE ND ICES

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 v

FIGU RES

Figure 1-1. San Francisco District (SPN) federal navigation projects (green) and traditional placement sites (orange [aqueous] and yellow [beneficial use])

Figure 1-2. San Francisco Bay historical (dark brown) and modern (light brown) baylands.

Figure 3-1. Potential sites for strategic placement across San Francisco Bay Figure 3-2. Alternative A: Eden Landing Ecological Reserve, Whale's Tail Marsh Figure 3-3. Alternative B: Emeryville Crescent Marsh Figure 3-4. Transport pathways from the dredging projects linked to the two alternatives to their Federal Standard and Section 1122 disposal sites for the two alternatives. Red designates Alternative A (Whale’s Tail Marsh), and yellow designates Alternative B (Emeryville Crescent Marsh)

Figure 3-5. Haul routes from Redwood City Harbor to the nearshore Eden landing placement site

Figure 3-6. Haul Routes from Oakland Harbor to the nearshore Emeryville Crescent placement site

Figure 3-7. Strategic placement sites narrowed down from twelve to two: Emeryville (top) and Eden Landing (bottom). Site map includes both placement footprint (red grid) and target marsh for restoration (aqua hatch)

Figure 3-8. Predicted percentage of dredged sediment mass and dredged material volume in each region at the end of the 2-month simulations for evaluating the placement volume in the shallow/east placement footprint

Figure 3-9. Binned regions to determine sediment transport fate from strategic placements toward target mudflats and marshes, ancillary mudflats and marshes, federal navigation channels, and flood control channels

Figure 3-10.Eden Landing shallow/east placement planview indicating sediment deposition thickness after a two-month summer model run for 100,000 CY.

Note that deposition thickness is on the order of one to two millimeters in the target mudflat and marsh complex

Figure 3-11.Predicted percentage of dredged sediment mass in each region during the 2-month simulations for the initial three Emeryville scenarios (left) and Eden Landing scenarios (right)

Figure 3-12.Placement cells in shallow water approximately two miles off the marsh at Eden Landing (i.e., Whale’s Tail) for the Shallow/East placement. The black outline represents the entire placement grid, while the blue and yellow cells represent the Eden Landing Shallow/East placement footprint cells with five vi and four placements respectively depending on the water depths and tidal timings

Figure 3-13.Strategic shallow-water placement cross-sectional conceptual model (Stantec and SFEI 2017)

Figure 3-14.Inorganic sediment supply to mudflats and marshes (SFEI 2015). This pilot project aims to mimic the way sediment moves with waves and tides from the shallow subtidal to the mudflats and marshes

Figure 3-15.Placement cells in shallow water approximately 2/3rd mile off the marsh at Emeryville Crescent for the Shallow/East placement. The black outline represents the entire placement grid, while the blue and yellow cells represent the Emeryville Crescent Shallow/East placement footprint cells with 10 and 9 placements respectively depending on the water depths and tidal timings

Figure 4-1. Present-day habitats at Whale's Tail Marsh (source: Ecoatlas) Figure 4-2. Present-day habitat at Emeryville Crescent Marsh (source: Ecoatlas) Figure 4-3 SSCs at Eden Landing east placement site relative to baseline conditions Figure 4-4 SSCs at Emeryville Crescent east placement site relative to baseline conditions.

Figure 4-5. Eelgrass mapped near Emeryville Crescent placement area (shown in light blue polygon). Data collected in 2003, 2009, 2014, and 2019. The blue buffers indicate Eelgrass Growth Buffers of 45 m accounting for patchiness, temporal variation and potential expansion). (Source: Bay Conservation and Development Commission (BCDC) SF Bay Eelgrass Impact Assessment Tool) 69

Figure 4-6. Eelgrass mapped near Eden Landing placement area (shown in blue polygon).

Includes data from surveys conducted in 2003, 2009, 2014, and 2019. The blue buffers indicate Eelgrass Growth Buffers of 45 m accounting for patchiness, temporal variation and potential expansion). (Source: BCDC SF Bay Eelgrass Impact Assessment Tool)

Figure 4-7. Community vulnerability proximal to project site two miles west of Eden Landing Ecological Reserve (BCDC Mapping Tool, 2020)

Figure 4-8. Community vulnerability in nearshore environment west of Emeryville, Alameda County (BDCD Mapping Tool, 2020) vii

TAB LE S

Table 1-1. Section 1122 11–point checklist Table 3-1. Initial site selection – the checks mark appliable criteria Table 3-2. First round modeling scenarios testing placement locations, scow volumes, and tidal timings at Emeryville and Eden Landing locations Table 3-3. Second round of modeling scenarios testing the effect of different placement volumes, seasonality, alternate sediment sourcing and footprint sizes at the Eden Landing location

Table 3-4. Summary of Impacts to Waters of the United States, including Wetlands Table 4-1. NAAQS, EPA Yearly Significance Thresholds, CAAQS, and BAAQMD thresholds that are effective in the project area Table 4-2. Air Quality Analysis Results Table 4-3. Alternative A and B Emissions Compared to No Action Alternative Emissions.

Table 4-4. CO2EQ Conversion Equation Table 4-5. GHG Emissions Inventory Results Table 4-6. Potential direct and indirect impacts and recovery times for aquatic species. 63 Table 4-7. Special Status Species, Critical Habitats, and EFH potentially occurring in and adjacent to the proposed action area Table 4-8. Example of fish species found in the different depth classes of the San Francisco

Estuary Table 5-1. Geographic areas that would be affected by the strategic shallow-water placement project Table 5-2. Past, Present, and Reasonably Foreseeable Future Projects Table 6-1. Summary of environmental compliance with applicable laws Table 7-1. Community and community-based organization contact details Table 7-2. Agency engagement details Table 7-3. Tribal contact details for required consultations under Section 106 of the

National Historic Preservation Act Table 7-4. Other relevant project communications Table 9-1: Summary of Potential Effects of the Recommended Plan viii

AC RON YMS, INIT IALISMS , AND ABB RE VIATIONS

APE Area of Potential Effects AWOIS Automated Wreck and Obstruction Information System BAAQMD Bay Area Air Quality Management District BCDC Bay Conservation and Development Commission BMPs Best Management Practices BUDM Beneficial Use of Dredged Material CAA Clean Air Act CAAQS California Ambient Air Quality Standards CDFW California Department of Fish and Wildlife CESA California Endangered Species Act CEQA California Environmental Quality Act CM Centimeters CO2EQ Carbon Dioxide Equivalents CRHP California Register of Historic Places CVL Confederated Villages of Lisjan CWA Clean Water Act CY Cubic Yards CZMA Coastal Zone Management Act DMMO Dredged Material Management Office EA Environmental Assessment EBDA East Bay Dischargers Authority EDER Eden Landing Ecological Reserve EFH Essential Fish Habitat EIR Programmatic Environmental Impact Report EIS Environmental Impact Statement ER Engineering Regulation ESA Endangered Species Act EWN Engineering With Nature FESA Federal Endangered Species Act FMP Pacific Groundfish Fisheries Management Plan FONSI Finding of no Significant Impact FTA Federal Transit Administration FWCA Fish and Wildlife Coordination Act FWS Fish and Wildlife Service GHGs Greenhouse Gases IS Initial Study LTMS Long Term Management Strategy MBTA Migratory Bird Treaty Act MHEA Middle Harbor Enhancement Area MHHW Mean Higher High Water MLLW Mean Lower Low Water MMPA Marine Mammal Protection Act MSC Main Ship Channel MSFCMA Magnuson Stevens Fishery Conservation and Management Act MTL Mean Tidal Level ix

NAAQS National Ambient Air Quality Standards NAHC Native American Heritage Commission NAVD North American Vertical Datum NEPA National Environmental Policy Act NMFS National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NTU Nephelometric Turbidity Units NUAD Not Suitable for Unconfined Aquatic Disposal O&M Operations and Maintenance PCBs Polybrominated Diphenyl Ethers RMP Regional Monitoring Program ROG Reactive Organic Gases RWQCB Regional Water Quality Control Board SBSP South Bay Salt Ponds SBSPRP South Bay Salt Ponds Restoration Project SF Bay San Francisco Bay SFEI San Francisco Estuary Institute SF-11 Alcatraz Island Disposal Site SF-DODS San Francisco Deep Ocean Disposal Site SHPO State Historic Preservation Offices SLR Sea-Level Rise SPN San Francisco District SPUR San Francisco Bay Area Planning and Urban Research Association SSC Suspended Sediment Concentration TSS Total Suspended Solids USACE U.S. Army Corps of Engineers USEPA United States Environmental Protection Agency USFWS United States Fish and Wildlife Service USGS United States Geological Survey WRDA Water Resources Development Act

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1 PR O P O S ED PR O J EC T

1.1 IN TROD U C T I ON

This environmental assessment (EA) initial study (IS), and mitigated negative declaration (MND), hereafter referred to as the EA/IS/MND, for the SAN FRANCISCO BAY

STRATEGIC SHALLOW-WATER PILOT PROJECT is written in compliance with the National Environmental Policy Act (NEPA) of 1969 (42 U.S.C. § 4321 et seq), as amended; the California Environmental Quality Act (CEQA) of 1970 (Pub. Res. Code, §§ 21000 et seq.), Regulations for Implementing the Procedural Provisions of the NEPA (40 C.F.R. §§1500- 1508), U.S. Army Corps of Engineers (USACE) Planning Regulations (Engineering Regulation (ER) 200-2-2), and the Guidelines for Implementation of CEQA (Title 14, California Code of Regulations § 15000 et seq). It is tiered off the document Programmatic Environmental Assessment And Finding of No Significant Impact For Implementation of Section 1122 of the Water Resources Development Act of 2016 Selection of Recommended Projects1. It evaluates the potential impacts associated with strategically placing approximately 100,000 cubic yards (CY) of dredged sediment from a federal navigation channel over approximately 19 – 562 days using a clamshell dredge and a dump scow at a shallow-depth (9 - 12 feet[ft]), in southern San Francisco Bay to leverage natural, in-bay, hydrodynamic processes for transporting sediments to existing mudflats and marshes.

This proposed project addresses tidal mudflat and salt marsh responses to strategic sediment placement at one South-Bay location.

1.2 DE SC RI P T I O N A ND LO C ATI ON

The proposed project is in San Francisco Bay (SF Bay or the Bay) in Northern California, which is a large tidal estuary receiving the outflow of large rivers (e.g., Sacramento and San Joaquin Rivers) and their respective watersheds. Approximately 40% of California’s water drains into SF Bay from the Sierra Nevada Mountain Range and the State’s Central Valley, which ultimately connects with the Pacific Ocean via the Golden Gate Strait under the Golden Gate Bridge. In particular, the proposed project location comprises tidal mudflats, salt-water tidal marshes, and subtidal shallow-water environments at the southern end of SF Bay. It is located two miles west of Eden Landing Ecological Reserve and approximately four miles west of the City of Hayward in Alameda County and is bounded by the San Mateo Bridge to the north and the southern shoreline of the Bay to the south.

The proposed project would place sediment dredged from a federal in-bay navigation channel in shallow waters on the periphery of the Bay to examine the ability of tides and currents to move the placed material to existing mudflats and marshes. This aquatic

1 https://usace.contentdm.oclc.org/utils/getfile/collection/p16021coll5/id/7252 2 The range of 19 – 56 days was calculated assuming a 400 CY/hour maximum production rate for a clamshell dredge plant and the corresponding range of 1 – 3 placements using 900 CY scows every high tide with two high tides per day. This resulted in between 1,800 – 5,400 CY/day of dredged material placement at the placement site, and consequently, 19 – 56 days to achieve the target 100,000 CY of dredged material.

https://usace.contentdm.oclc.org/utils/getfile/collection/p16021coll5/id/7252

~11~ placement technique – placing dredged sediment in shallow water in the nearshore adjacent to a tidal wetland and utilizing natural hydrodynamic and morphodynamic processes to move the sediment onto the mudflat and marsh – is referred to as strategic shallow-water placement. This strategic shallow-water placement pilot project is expected to move a portion of the placed sediment to the mudflats and the marsh plain, mimicking natural sediment supply to wetland ecosystems to improve habitat. Monitoring will be integrated to evaluate the success of the pilot project and its environmental effects.

1 .2 .1 Federal Navigation Projects

As part of its Operations and Maintenance (O&M) dredging program in the SF Bay area, USACE annually dredges four federal channels (Suisun, Richmond Inner Harbor, Oakland Harbor, and Main Ship Channel [MSC]), biannually dredges three federal channels (Pinole Shoal, Redwood City Harbor, and Richmond Outer Harbor), and periodically dredges several other federal channels (Figure 1-1). This project proposes sourcing dredged sediment from either Redwood City Harbor or Oakland Harbor federal navigation channel for strategic placement.

Figure 1-1. San Francisco District (SPN) federal navigation projects (green) and traditional placement sites (orange [aqueous] and yellow [beneficial use]).

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1.3 PU R P O S E A N D NE ED FO R PROP OS E D AC T I O N

The purpose of the proposed action is to determine the effectiveness of strategically placing dredged sediment in the nearshore, shallow water environment to maximize sediment transport to existing tidal mudflats and tidal marshes while minimizing ecological impacts to benthic habitats and environmental resources. Specifically, the proposed project aims to assess the ability of this novel sediment placement technique to transport sediment onto target mudflats and marshes.

Need – To capitalize on the opportunity to enhance sea-level-rise resilience for tidal mudflats and salt marshes by beneficially using material dredged from SF Bay navigation channels using an innovative placement method that has not been used in SF Bay.

The San Francisco Baylands (e.g., mudflats, marshes, and other intertidal habitats) protect the adjacent communities, improve water quality, and provide habitat for thousands of fish and wildlife species, including several endangered and special-status species. Before 1850, the SF Bay region included 200,000 acres of tidal wetlands (including salt marsh, brackish, and freshwater wetlands) (Figure 1-2). However, historical loss of these landscapes to development has drastically reduced the acreage of such habitats across San Francisco Bay. The region has lost over eighty-five percent of that acreage through diking, dredging, and development. In addition, Sea-Level Rise (SLR) and sediment deficits further threaten long-term bayland sustainability.

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Figure 1-2. San Francisco Bay historical (dark brown) and modern (light brown) baylands.

Efforts are underway to restore these baylands with sediment from other locations.

(Dusterhoff et al. 2021) of the San Francisco Estuary Institute (SFEI) estimate the Bay’s tidal marshes and mudflats will need approximately 450 million CY of sediment between now and 2100 to maintain existing tidal marshes and those currently slated for restoration.

Sediment dredged from federal navigation channels represents a significant source of supply available for restoration. The practice of beneficially using these sediments to restore marshes already exists and has been successfully implemented (i.e., beneficial use of dredged material or (BUDM)). Federal, state, and local agencies and organizations are currently on track to restore 60,000 acres of tidal wetlands to augment 40,000 already-restored acres. The resulting 100,000 acres will help protect the region from tidal flooding and reduce storm damage, especially if SLR continues as predicted or accelerates, as well as protect habitat for endangered species.

These agencies, through a variety of partnerships, have acquired land, developed regional plans, conducted environmental reviews, received permits, and are implementing multiple projects to restore critical tidal wetlands for both ecosystem benefits and shoreline protection. Meeting the goal of wetland climate resilience, however, will require optimization on several levels, including finding least cost methods with streamlined and

~14~ more efficient permitting processes to match dredged material with potential placement site characteristics and capacities.

In the SF Bay area, the current paradigm of BUDM is to place material directly on diked, subsided baylands to raise site elevations to adjacent marsh plains prior to tidal breaching, thereby supporting rapid development of tidal marsh vegetation and habitat. Subsided restoration sites that are breached without raising site elevations are projected to take 60– 75 years to develop into tidal marsh, while direct placement BUDM can cut development time down to 10–15 years. This is important because restored marshes breached without sufficient sediment supply may not accrete fast enough prior to increased rates of SLR in the future. Although direct placement is a critical tool for subsided baylands, it can be a costly restoration strategy, and given the projected increase in SLR, the SF Bay region is actively experimenting with new tools to complement and add to the regional toolbox of BUDM actions, particularly those that reduce cost by working with existing natural processes that drive tidal marsh development and resilience under current and future SLR conditions. Shallow-water placement or thin-layer placement are alternative BUDM practices.

The targeted areas for strategic shallow-water placement are locations on the margins of the Bay adjacent to marshes and mudflats in need of sediment. Shallow water ranges from near the bayward edge of the mudflat (around Mean Lower Low Water (MLLW), which is approximately 0 feet North American Vertical Datum [NAVD]) to the top of the deep channel (a depth of about 13 feet NAVD).

1.4 BAS I C AN D OV E R A L L PROJ E C T PUR P O S E

This EA includes a 404(b)(1) analysis. Under Section 404 of the Clean Water Act (CWA), USACE is granted permitting authority for any activity that would involve the discharge of dredge or fill materials into waters of the U.S., including wetlands (33 U.S.C. § 1344). The section 404(b)(1) guidelines prohibit discharge of dredged or fill material if a practicable alternative to the proposed project exists that would have less adverse impacts on the aquatic ecosystem, including wetlands, so long as that alternative does not have other significant adverse environmental consequences. The USACE does not issue itself a permit for its actions involving the discharge of dredge or fill material to waters of the U.S., but instead integrates an equivalent 404(b)(1) analysis in its NEPA documentation.

1 .4 .1 Basic Project Purpose

The basic purpose is to ascertain the feasibility of using strategic, in-water sediment placement to maintain mudflats and tidal marshes. This is a water-dependent project under Section 404(b)(1).

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1 .4 .2 Overall Project Purpose

The overall purpose of the Strategic Shallow Water Placement Pilot Project is to test a novel approach to increase mudflat and tidal marsh resilience to SLR in SF Bay via strategic placement of sediment dredged from federal navigation channels at a shallow, in-Bay location adjacent to the mudflat and tidal marsh. This Engineering with Nature (EWN) approach will augment sediment supply in a sediment-starved system to leverage existing morphodynamic processes to transport sediment toward mudflat-marsh systems for habitat enhancement. The goal is to determine if this EWN approach can be a successful, low-cost method to achieve BUDM. The overall project purpose is to ascertain whether placing sediment derived from maintenance dredging of an in-Bay federal navigation channel at a shallow, subtidal location in SF Bay adjacent to the intertidal mudflat and marsh to help sustain these critical ecosystems faced with SLR and limited sediment supply (i.e., BUDM). This project aims to understand the impacts to benthic (i.e., Bay bottom) habitats and communities; the spatial extent of the effect zone; the temporal scale of disturbance and recovery time; and to monitor its effects on eelgrass beds, oyster beds, or similar environmental resources.

This project also aims to understand the scale of sediment deposition post-placement at the placement site, on the intertidal mudflat, and on the adjacent tidal marsh; and the wind, wave, and sediment flux conditions pre- and post-placement across the interconnected subtidal-mudflat-marsh complex. This project will include robust monitoring protocols using appropriate methods and techniques to determine sediment deposition and impacts (beneficial or adverse) resulting from strategic placement.

1.5 STU DY AU T HOR I T Y

The beneficial use of material dredged from a SF Bay federal navigation channel and placed in shallow bay water is authorized by Section 1122 of the Water Resources Development Act (WRDA) 2016. Section 1122 requires USACE to establish ten pilot projects, nationwide, that beneficially use dredged material. According to Section 5 of the Implementation Guidance, each pilot project is to serve different purposes as identified in Section 1122(a):

a. Reducing storm damage to property and infrastructure;

b. Promoting public safety;

c. Protecting, restoring, and creating aquatic ecosystem habitats;

d. Stabilizing stream systems and enhancing shorelines;

e. Promoting recreation;

f. Supporting risk management adaptation strategies; and

g. Reducing the costs of dredging and dredged-material placement, such as projects that use dredged material for:

1. Construction or fill material;

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2. Civic improvement objectives; and

3. Other innovative uses and placement alternatives that produce public economic or environmental benefits.

This pilot project addresses Implementation Guidance Sections 5.c, 5.d, and 5.g.3 and satisfies the Implementation Guidance 11-point Checklist requirements for Pilot Project Implementation:

Table 1-1. Section 1122 11–point checklist

REQUIREMENT COMMENT

1 Clear description of the recommended plan; §1.2 2 Demonstration of the project justification based on standard Corps project justification criteria for the project purpose in accordance with the general guidance applicable to the project purpose(s)

Followed the USACE planning process to maximize ecological benefits. Project outputs expected to help the Enterprise deliver on the intent of §204 in a more cost-effective way.

3 Documentation of compliance with appropriate federal, state, and local environmental and regulatory requirements such as NEPA, and other environmental laws normally included in a feasibility study specifically authorized by Congress

Table 6-1

4 Documentation of compliance with policies applicable to Section 204 of the Continuing Authorities Program

Yes: no cost share involved

5 Completed Real Estate Plan consistent with Chapter 12 of ER 405-1-

Completed by Kelly Boyd, SPL (Appendix E)

6 The non-federal sponsor financial analysis and financing plan at a level of detail appropriate to the scale of the project.

Not Applicable: the project is 100% federally funded

7 District Real Estate certification that the non-federal sponsor has the capability to acquire and provide the required real estate interests

Not Applicable: USACE claims navigational servitude, plus the land use is temporary

8 Detailed description of the non-federal sponsor's local cooperation requirements

Not Applicable: the project is 100% federally funded

9 Identification of the anticipated operation, maintenance, repair, replacement, and rehabilitation activities, including estimated costs;

Not applicable: one-time sediment-placement experiment

10 District Counsel statement of legal sufficiency for the decision documentation and compliance with NEPA and other applicable environmental laws.

Provided by SPN Office of Counsel

11 Approval of the report and the environmental compliance decision documents are delegated to the MSC commander.

Acknowledged

2 S C O P E O F AN ALY S IS

This EA/IS/MND presents an analysis of potential impacts (direct, indirect, and cumulative) on resources consistent with NEPA and CEQA. Section 4 analyzes effects to physical, biological, and human resources. The alternatives analysis, located in this study’s Decision Document, describes the screening process for shallow water dredged material placement and site selection.

2 . 1 DIR EC T IM PAC T S

A direct impact is caused by the action and occurs at the same time and place as the action. In San Francisco Bay, shallow-water, dredged-material placement, can have several direct impacts, such as bathymetric change, sediment mismatch, increased noise and boat traffic, temporary subtidal and intertidal burial, and temporary increased turbidity and

~17~ suspended-sediment concentration. These actions are immediate – i.e., contemporaneous with dredged-material placement.

Geographically, direct impacts will be confined to surface waters in the transport area where it deviates from the route taken to reach the federal-standard site; the nearshore aquatic environment, mudflat, and marsh at the project site; and the air basin (emissions).

Temporally, direct impacts will be confined to the duration of placement activity, approximately between 19 – 56 days.

2 . 2 IN D I R EC T IM PAC T S

Geographically, indirect impacts will be confined to the nearshore aquatic environment, mudflat, and marsh at the project site; adjacent mudflats and marshes; and nearby parts of the Bay. Temporally, indirect impacts will end when the placed sediment has been dispersed, after project completion which is estimated to take 19 - 56 days, or when the fauna reestablish in the project area.

3 ALT E R NAT I VE S

In USACE planning, alternatives comprise one or more measures: a measure is a feature or an activity that can be implemented at a specific geographic location to address one or more planning objectives. Reasonable measures for the Strategic Placement Project include placement of dredged material from a federal navigation channel to a shallow nearshore site. The USACE planning process was followed to identify an initial array of alternatives, screen that array down to a final array of alternatives and select a plan – the proposed action.

To satisfy NEPA and CEQA requirements and provide the basis for the required 404(b)(1) alternatives analysis, three alternatives were evaluated as part of the EA/IS/MND. Alternatives assessed in the EA/IS/MND include the No Action Alternative (not placing material from a federal navigation channel at a shallow water site); and two action alternatives that involve placing material from a federal navigation channel strategically nearshore for beneficial use.

3 . 1 NO ACT IO N ALT E R N AT I VE

The No Action Alternative comprises placing material from a SF Bay federal navigation channel O&M project at its federal standard (i.e., base plan3) location. In the case of Redwood City Harbor, this material would be placed at the Alcatraz Island Disposal Site (SF-

3 The Federal Standard is defined in USACE regulations as the least costly dredged-material disposal or placement alternative (or alternatives) identified by USACE that is consistent with sound engineering practices and meets all federal environmental requirements, including those established under the Clean Water Act (CWA) and the Marine Protection, Research, and Sanctuaries Act (MPRSA) (see 33 CFR 335.7, 53 FR 14902). The term “Base Plan” is a more accurate operational description of the Federal Standard, because it defines the disposal or placement costs that are assigned to the “navigational purpose” of the project.

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11), the in-bay placement site near Alcatraz Island; in the case of Oakland Harbor, this material would be placed at the offshore location, San Francisco Deep Ocean Disposal Site (SF-DODS). In either case, the No Action Alternative would result in sediment being lost either to the deep ocean or dispersed to deeper subtidal, Bay environments. The consequence is a lost opportunity to maximize BUDM in the Bay.

3 . 2 PL A N FOR M U L ATI ON SU MMA RY

The USACE planning process is a structured approach to problem solving. Usually, it comprises six steps:

1. Identifying problems and opportunities;

2. Inventorying and forecasting conditions;

3. Formulating alternative plans;

4. Evaluating alternative plans;

5. Comparing alternative plans;

6. Selecting a plan.

Further discussion of the plan formulation analysis, process and selection of the proposed action is discussed in the Decision Document and Plan Formulation Appendix (Appendix B).

To reduce the number of potential shallow water placement sites from twelve (Figure 3-1), to two, eight criteria were applied (Table 3-1). These criteria include:

1. Eroding or drowning marsh; lack of natural sediment supply;

2. Sufficient wind-wave action to resuspend placed sediment;

3. Proximity to a federal channel;

4. Open to tidal exchange, existing marsh;

5. Water deep enough to get scow close to shore;

6. Resilience for shorelines near disadvantaged communities (DACs);

7. Lower populations of critical species;

8. Avoiding large eelgrass beds and nearshore reef projects.

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Figure 3-1. Potential sites for strategic placement across San Francisco Bay.

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Table 3-1. Initial site selection – the checks mark appliable criteria.

SITE (SOUTH

TO NORTH)

CRITERIA

REJECT

1. 2 3 4 5 6 7 8 Eroding or drowning marsh

Sufficient wind-wave action

Prox. to federal channel

Open to tidal exchange

Water deep enough

Shoreline resilience near DACs

Lower pop. Of critical species

Avoiding eelgrass & reef projects

Pond A6 Faber Tract

Cogswell Marsh

Eden Landing (Whale’s Tail)

Arrowhead

Emeryville Crescent

Bothin Marsh

Stege Marsh

Corte Madera

Giant

China Camp

Point Edith

3 . 3 TH E FI N A L ARRAY O F ALT ER N AT IV E S

After screening, ten of the sites were considered but eliminated from further NEPA analysis. Sites were eliminated because they would not meet the purpose and need for the action (i.e., they were unlikely to transport sediment onto target mudflats and marshes while minimizing impacts to environmental resources) or were infeasible. Screening criteria 1, 2, 4, 7, and 8 focused on site ability to meet the purpose and need, whereas criteria 3 and 5 focused on feasibility of implementation. Sites that did not meet most criteria were eliminated from the focused array and further study in the EA/IS/MND. Two alternative sites were carried forward (A: Eden Landing Whale’s Tail Marsh [Figure 3-2] and B: Emeryville Crescent Marsh [Figure 3-3]).

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Figure 3-2. Alternative A: Eden Landing Ecological Reserve, Whale's Tail Marsh

Figure 3-3. Alternative B: Emeryville Crescent Marsh

Sediment dredged from the Redwood City Harbor federal navigation channel will be the source for Whale’s Tail Marsh, and sediment dredged from the Oakland Harbor federal

~22~ navigation project will be the source for Emeryville Crescent Marsh (Figure 3-4). The federal-standard site for the former is SF-11; for the latter, it is SF-DODS.

Figure 3-4. Transport pathways from the dredging projects linked to the two alternatives to their Federal Standard and Section 1122 disposal sites for the two alternatives. Red designates Alternative A (Whale’s Tail Marsh), and yellow designates Alternative B (Emeryville Crescent Marsh).

Because the transport pathways to the two pilot sites cross shallow water rather than the deeper water used to go to the federal standard disposal sites, there is a higher potential for impacts to the bottom during transit. Figure 3-5 and Figure 3-6 show the transport pathways to the Whale’s Tail placement site and Emeryville Crescent site, respectively. Best Management Practices (BMPs)) should be employed to limit no spillage from the scows during transit. Tugs used to tow the scows, however, could stir up the bottom as they approach and maneuver through the placement site. We expect the impacts would be similar to the impacts of scow emptying, i.e., temporary and minor with short-term disruption to the habitat.

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Figure 3-5. Haul routes from Redwood City Harbor to the nearshore Eden landing placement site.

Figure 3-6. Haul Routes from Oakland Harbor to the nearshore Emeryville Crescent placement site.

3 . 4 MO D EL IN G

Next, the two action alternatives were analyzed using a quantitative modeling approach (i.e., the UnTRIM Bay-Delta model and the Short-Term Fate [STFATE] of dredged material in

~24~ open water model) to determine sediment fluxes, shear stresses, transport pathways, and deposition zones for different placement depths (i.e. locations) and volumes in the feasible placement grids (Figure 3-7) to refine the design of these alternatives. The modeling approach was used to consider various volume and depth scenarios at the two sites, and those scenarios that were less likely to move sediment onto target mudflats and marshes while minimizing impacts to environmental resources were eliminated.

Figure 3-7. Strategic placement sites narrowed down from twelve to two: Emeryville (top) and Eden Landing (bottom). Site map includes both placement footprint (red grid) and target marsh for restoration (aqua hatch).

Placement alternatives incorporated information on flood tides at various stages of the tidal cycle, including Mean Higher High Water (MHHW), Mean Sea Level (MSL), and MLLW, during the San Francisco Bay’s environmental dredging window (i.e., June 1 – November 30). This determined specific depths for each cell in the placement grid, and ultimately, the

~25~ design footprints based on depth isolines. The first set of alternatives all utilized the same placement volumes (i.e., 100,000 CY) distributed across the footprint based on scow loading capability as correlated with depths of greater than 9 feet for the shallowest placement; 10 feet for the intermediate placement; and 11 feet for deepest placement. In the first round of modeling, six placement alternatives were analyzed – three for Eden Landing and three for Emeryville Crescent Marsh. The first six scenarios were used to determine whether Emeryville or Eden Landing is most suitable for the pilot project.

Different placement strategies at each location were then analyzed to determine the second round of modeling scenarios, and ultimately, to narrow in on the most effective placement strategy (Table 3-2).

Table 3-2. First round modeling scenarios testing placement locations, scow volumes, and tidal timings at Emeryville and Eden Landing locations.

Scenario

Placement Grid

Location

Placement Volume

(103 CY)

Scow

(CY)

Minimum Time Between

PLACEMENTS

(HRS)

Notes

1 Emeryville Deep 100 1,400 6

2 Emeryville Middle 100 1,150 2 Placements during flood tide

3 Emeryville Shallow/East 100 900 2

4 Eden Landing Deep 100 1,400 5

5 Eden Landing Middle 100 1,150 1.5 Placements during flood tide

6 Eden Landing Shallow/East 100 900 1.5

The second round of modeling consisted of six scenarios to evaluate the effect of different placement volumes, seasonal differences (summer versus winter), alternate sediment sourcing, and placement footprints (Table 3-3).

Table 3-3. Second round of modeling scenarios testing the effect of different placement volumes, seasonality, alternate sediment sourcing and footprint sizes at the Eden Landing location.

Scenario

Placement Grid

Location

Placement

(103 CY)

Scow

VOLUME

(CY)

Minimum Time Between Placements

(HRS)

Notes

6 Eden Landing Shallow/East 100 900 1.5 From First Set 7 Eden Landing Shallow/East 50 900 1.5

8 Eden Landing Shallow/East 75 900 1.5

9 Eden Landing Shallow/East 100 900 1.5 Winter Placement 10 Eden Landing Shallow/East 100 900 1.5 Oakland Sediment 11 Eden Landing Expanded East 100 900 1.5

12 Eden Landing Expanded East 125 900 1.5

This second round of modeling first examined how efficient different placement volumes (50,000; 75,000; and 100,000 CY) were at Eden Landing assuming the Shallow/East placement strategy. Another sensitivity analysis examined 100,000 CY

~26~ placements subject to wind and wave climate conditions during summer and winter months. Modeling also examined placement sensitivity to the original east/shallow placement footprint versus an expanded east footprint that represented a hybrid of the shallow and intermediate depth scenarios with an overall footprint over twice the size of the original shallow-east size (Table 3-3). Different sediment source channels (i.e., Oakland Harbor versus Redwood City Harbor) were tested to understand the impact of different grain sizes on sediment resuspension and mobility, with coarse sediments from Oakland Harbor channel and fine sediments from Redwood City Harbor channel.

Finally, different placement volumes (100,000 CY versus 125,000 CY) were tested within this expanded east footprint.

Modeling results indicated that summer placements were more efficient at delivering sediments to the target mudflat and marsh system. Analysis of wave resuspension potential indicated significantly higher transport due to waves and wind speeds in summer months than in winter months. Significantly more placed sediment transported to Eden Landing mudflat/marsh complex in the two months following summer placement than in the three months following winter placement. There was also more regional sediment transport north out of South Bay following winter placement. Dredged material placements earlier in the summer when wind speeds are seasonally high are likely to be more effective at transporting sediment into the marsh than late-fall and winter placements.

Larger placement volumes resulted in more sediment reaching the target mudflat and marsh on short time scales (on the order of one to two millimeters) and will therefore be more measurable to determine pilot project success, although millimeter-scale deposition is difficult to measure over a wide area. Placement volume and mudflat and marsh deposition volume were linearly correlated with higher detectability for the 100,000 CY placement at the shallow/east footprint (Figure 3-8). A larger fraction of Oakland Harbor sediment remains in the placement footprint at the end of the two-month analysis period. Dredged material with lower sand content is better for strategic placement, but the differences between dredged material from Oakland Harbor and Redwood City Harbor do not have a large effect on the overall volume of sediment that reaches Eden Landing after two months.

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Figure 3-8. Predicted percentage of dredged sediment mass and dredged material volume in each region at the end of the 2-month simulations for evaluating the placement volume in the shallow/east placement footprint.

The expanded footprint includes areas of greater depth than the original footprint but allowed for thinner placements over the placement footprint. Less sediment was transported out of placement footprint in the two months following placement for the expanded footprint. Overall, results indicate that placements closest to the target marsh at the shallowest depths possible, where wave energy is highest, are most effective at transporting sediment to the marsh.

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The final site selection process analyzed the percentage and volume of sediment delivered to the transition intertidal mudflat and upland marsh, as well as the percentage dispersed outside the placement footprint but not to the target locations (i.e., nearshore intertidal mudflat and adjacent marsh) and the percentage re-deposited in federal navigation channels or in nearby flood control channels (Figure 3-9). These criteria describe the efficiency and impacts of each design alternative, with the goal of maximizing sediment deposition to tidal flats/marshes, and minimizing sediment lost to the Bay, navigation channels and flood control channels. Modeling results indicated that the 100,000 CY shallow/east placement alternative at Eden Landing in the summer months using dredged material from the Redwood City Harbor federal navigation channel was the optimal strategy, which corresponds to scenario 6 (Figure 3-10, Figure 3-11, Table 3-2, Table 3-3).

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Figure 3-9. Binned regions to determine sediment transport fate from strategic placements toward target mudflats and marshes, ancillary mudflats and marshes, federal navigation channels, and flood control channels.

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Figure 3-10. Eden Landing shallow/east placement planview indicating sediment deposition thickness after a two-month summer model run for 100,000 CY. Note that deposition thickness is on the order of one to two millimeters in the target mudflat and marsh complex.

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Figure 3-11. Predicted percentage of dredged sediment mass in each region during the 2-month simulations for the initial three Emeryville scenarios (left) and Eden Landing scenarios (right).

3 . 5 PROP OS ED AC TI ON

Based on the sediment-transport modeling discussed above, Eden Landing shallow/east 100,000 CY summertime placement was designated as the Proposed Action.

3 .5 .1 Eden Landing Whale’ s Tail Marsh ( Alternative A: Proposed Action)

Under this alternative the proposed action would place approximately 100,000 CY of sediment from a SF Bay federal O&M dredging project in a shallow-water placement area adjacent to the mudflat and marsh at Eden Landing (Figure 3-12) to evaluate the ability of tides and currents to move dredged sediment placed in the nearshore environment to the adjacent mudflat and marsh (Figure 3-13, and Figure 3-14).

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Figure 3-12. Placement cells in shallow water approximately two miles off the marsh at Eden Landing

(i.e., Whale’s Tail) for the Shallow/East placement. The black outline represents the entire placement grid, while the blue and yellow cells represent the Eden Landing Shallow/East placement footprint cells with five and four placements respectively depending on the water depths and tidal timings.

Figure 3-13. Strategic shallow-water placement cross-sectional conceptual model (Stantec and SFEI 2017).

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Figure 3-14. Inorganic sediment supply to mudflats and marshes (SFEI 2015). This pilot project aims to mimic the way sediment moves with waves and tides from the shallow subtidal to the mudflats and marshes.

Throughout one dredging episode (i.e., the entirety of channel dredging in any one year) of the Redwood City Harbor O&M Project, scows with dredged material will be diverted from the federal standard placement site SF-11 (Figure 1-1). Placement, which is estimated to take between 19 – 56 days, will occur during the scheduled O&M dredging and will finish before the end of the work window on November 30.

Typical dimensions for the scows placing sediment are approximately 180 ft (length) by 50 ft (breadth). The material will be placed at the in-bay, strategic placement site with a target thickness between about 0.33 ft and 1 ft. Based on wave and current modeling, it is expected that the scows will need to unload in water depths between 9 and 12 feet in absolute depths (i.e., placement location will vary depending on the stage of the tide, or how deep the water is at any given point) to maximize marsh-ward transport by waves and currents. The total volume of placed material will be approximately 100,000 CY, and placements will occur during flood tides in an approximately 9,700 feet long and 630 feet wide placement footprint (138-acres – comprised by the polygon of yellow and blue grid cells in Figure 3-12) that was determined by computer modeling and geospatial analysis to be most suitable for successful dispersal. Scows, which will be light loaded to approximately 900 CY, will make approximately 112 round trips between Redwood City and the placement site, taking between 19 – 56 days. The placement area and adjacent mudflat-marsh complex will be monitored before and after placement.

3 .5 .2 Emer yvi l le Crescent Marsh ( Alternative B)

Under this alternative the proposed action would place approximately 100,000 CY of sediment from Oakland Harbor in a shallow-water placement area adjacent to the mudflat and marsh at Emeryville Crescent (Figure 3-15) to evaluate the ability of tides and currents to move dredged sediment placed in the nearshore environment to the adjacent mudflat and marsh (Figure 3-13 and Figure 3-14). During O&M dredging of Oakland Harbor scows with dredged material would be diverted from the federal standard placement site SF- DODS (Figure 1-1). Typical dimensions for the scows placing sediment are approximately

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180 ft (length) by 50 ft (breadth). The material would be placed at the shallow water strategic placement site with a target thickness between about 0.33 ft and 1 ft. Based on wave and current modeling, the scows would need to unload in water depths less than 10 ft in absolute depth (i.e., placement location will vary depending on the stage of the tide) to maximize marsh-ward transport by waves and currents. The total volume of placed material would be approximately 100,000 CY, and placements would take place during flood tides within an approximately 2,500 feet long and 1,250 feet wide placement footprint (69 acres) that was determined by computer modeling and geospatial analysis to be most suitable for successful placement (Figure 3-15 shows the target placement areas shaded in blue and yellow). Scows, which will be light loaded to approximately 900 CY, will make approximately 112 round trips between Oakland Harbor federal navigation channel and the Emeryville Crescent Marsh placement site.

Figure 3-15. Placement cells in shallow water approximately 2/3rd mile off the marsh at Emeryville Crescent for the Shallow/East placement. The black outline represents the entire placement grid, while the blue and yellow cells represent the Emeryville Crescent Shallow/East placement footprint cells with 10 and 9 placements respectively depending on the water depths and tidal timings.

3 . 6 CL E A N WAT E R AC T ( 404) ALT E R N AT IV ES AN A LYS I S

In evaluating its projects under Section 404 of the CWA, USACE must clearly demonstrate that there are no practicable, less-damaging alternatives than the Proposed Action. The USACE is responsible for making the formal determination of compliance with the 404 (b)(1) Guidelines.