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2003-27703S Phase 2 – South Bay Salt Pond Restoration Project

Posted: 4/18/2017

Expiration date: 5/17/2017


1. INTRODUCTION:

The U.S. Fish and Wildlife Service (USFWS, Federal Lead Agency) and the California State Coastal Conservancy (POC: John Bourgeois, 408-314-8859), 1515 Clay Street, 10th Floor, Oakland, CA 94612, through its agent, AECOM (POC: Dillon Lennebacker, 510-874-3035), 300 Lakeside Drive, Oakland, CA 94612, has applied to the U.S. Army Corps of Engineers (USACE), San Francisco District, for a Department of the Army Permit to conduct work within the Corps’ jurisdiction to implement Phase 2 of the South Bay Salt Pond (SBSP) Restoration Project within USFWS Don Edwards National Wildlife Refuge. Phase 2 involves discharge of fill within former salt ponds for habitat restoration, flood risk management and wildlife-oriented public access. This Department of the Army permit application is being processed pursuant to the provisions of Section 404 of the Clean Water Act of 1972, as amended (33 U.S.C. § 1344 et seq.), and Section 10 of the Rivers and Harbors Act of 1899, as amended (33 U.S.C. § 403 et seq.).



2. PROPOSED PROJECT:

Project Site Location: Phase 2 activities are proposed in four former salt pond complexes: Alviso-Island Ponds (A19, A20, &A21) (lat. 37.464876, long. -121.970986), Alviso-A8 Ponds (A8 & A8S) (lat. 37.428778, -121.991558), Alviso–Mountain View Ponds (A1 & A2W) (lat. 37.442525, -122.086577), and the Ravenswood Ponds (R3, R4, R5 & S5) (lat. 37.493048, -122.161933). The nearly 2,400 acres of salt ponds are located in San Mateo, Santa Clara and Alameda Counties (see Figures 1 and 2).

Project Site Description: The project sites are former salt ponds on the shores of the South Bay, with surrounding levees and some fringing marshes.

Alviso-Island Pond Cluster: The three Alviso-Island Ponds were breached to Coyote Creek and tidal action in March 2006. Once breached, these ponds provided intertidal foraging habitat for shorebirds and other waterbirds at low tide and tidal foraging habitat for waterfowl at high tide. As sediment has accumulated, tidal marsh vegetation is becoming established, providing breeding and foraging habitat for the California Ridgway’s rail (recently noted in Pond A21) and other marsh species. Though ruderal in their vegetation species composition, upland portions of the levees may provide suitable habitat for a range of species that need high-tide refugia. The outboard margins of the pond levees (on Mud Slough and Coyote Creek) are characterized by seasonally brackish marsh.

Alviso-A8 Pond Cluster: Ponds A8 and A8S were physically connected in the Phase 1 actions and were made “reversibly muted tidal habitat”. The ponds provide forage habitat for terns, waterfowl and shorebirds and the levees provide nesting habitat. Sediment has been accreting in these ponds since they were opened to muted tidal flows through culverts and a variable-size, reversible armored notch in 2011. Though they are muted tidal, the ponds provide habitat for fish and benthic invertebrates that provide food for a variety of species. Ponds A8 and A8S provide flood storage basins during high-rainfall events.

Alviso-Mountain View Pond Cluster: The outboard areas of the pond levees and the lower reaches of the surrounding sloughs are characterized by tidal salt marsh and the interior of these ponds are primarily open water or mudflat with little to no visible vegetation. Suitable nesting bird habitat for California gulls (Larus californicus), Forster’s terns (Sterna forsteri), American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanu), and the occasional black skimmer (Rynchops niger) exists on a few small, isolated islands found within the interior waters of Ponds A1 and A2W.

Ravenswood Pond Cluster: The ponds are bordered by Bedwell Bayfront Park to the west, SR 84 and the city of Menlo Park to the south, Ravenswood Slough to the east, and Greco Island and open Baywater to the north. Ponds R3 and R4 are seasonally wet ponds that collect rainwater during winter but dry out to become salt panne in summer. The upland and remnant slough channels and borrow ditches within the ponds have extremely high salinity, which inhibits most plant life but the salt flats do provide nesting habitat for special-status species including the threatened western snowy plover (Charadrius alexandrinus nivosus). Vegetation growing on the pond bottom is limited to extremely salt-tolerant vegetation, notably small flowered iceplant, which are an invasive species requiring active and regular control efforts. Ponds R5 and S5 are seasonally wet ponds that collect rainwater during winter but dry out to become salt pannes in summer. They contain little to no vegetation. A drainage outlet for stormwater runoff from the Bayfront Canal and Atherton Channel in portions of Redwood City, Atherton, and Menlo Park carries water into Flood Slough next to the southern exterior of Pond S5, creating freshwater to brackish marsh habitat on the water’s way to the Bay.

Project Description: As shown in the Figures 3-6, the applicant proposes the following actions to enhance habitat at all four pond clusters, maintain or increase flood risk management and provide additional public access and recreation at two of the pond clusters.

Habitat Enhancement. Figures 3-6 show the features proposed for habitat enhancement at the project sites. At Alviso-Island Pond Cluster (Figure 3), the project would lower, remove or breach levees at Ponds A19 and A20 to increase habitat connectivity, enhance tidal flows, and expedite the transition to tidal marsh. Excavated material from the levee modifications would be used to establish ditch blocks or placed into the ponds’ borrow ditches, including six ditch blocks in Pond A19. Fill placed in Corps jurisdiction would remain below MHW.

At Alviso-A8 Pond Cluster (Figure 4), the project would build habitat transition zones at the southwest and southeast corners of Pond A8S to provide a range of benefits, including habitat complexity and diversity, erosion protection and preparation for long-term sea-level rise adaptation. The tops of the habitat transition zones would be approximately 9 feet elevation NAVD88 and the lengths along the MHHW line would be 2,075 linear feet each, separated to allow potential future connections with San Tomas Aquino Creek. The habitat transition zones would be constructed of fill from upland construction projects and would extend to the center of the pond at a slope of 30:1, typically.

At Alviso-Mountain View Pond Cluster (Figure 5), the project would breach existing levees at two locations in A1 and four locations at A2W to connect the ponds to surrounding sloughs and allow tidal action, sediment accretion and vegetation establishment. Habitat transition zones and up to ten habitat islands would be constructed in A1 and A2W. The habitat transition zones, once vegetated, would provide habitat for the salt marsh harvest mouse (Reithrodontomys raviventris ) and other terrestrial species, and would provide a gentle slope to dissipate wave energy and reduce erosion. The habitat islands would provide nesting and roosting habitat for shorebirds, terns and dabbling birds. The habitat transition zones and islands would be constructed largely of upland fill from off-site projects. Roughly 3,700 linear feet and 3,200 linear feet of transition zone would be established along the inside slope of Ponds A1 and A2W, respectively. The habitat transition zones would have a top elevation of approximately 9 feet NAVD88. The slope of these features in Pond A1 would be varied to provide a range of different slopes including slopes at 10:1, 20:1, 30:1 and 40:1 (h:v). This variation would provide observational data about the habitat values, erosion protection, and sea-level rise adaptation that would result from these varying slopes. In Pond A2W, the slope would be 30:1 (h:v). The habitat islands would have a top area of roughly 10,100 square feet, a top elevation of 12.5 feet NAVD88 (roughly 3 feet above MHHW) and side slopes would be approximately 3:1 (h:v). As the ponds transition to marsh, the island habitat would eventually become marsh mounds.

At Ravenswood Pond Cluster (Figure 6), the project would install four water control structures (pipe culverts through levees), between ponds R3, R4, R5, S5 and Flood and Ravenswood Sloughs, which would allow the ponds to be managed for enhanced habitat for the different bird species. The project would remove most of the internal levees in R5 and S5, and would breach the northeastern corner of R4, lower the levee in the northwest corner and excavate a pilot channel to increase water movement and connectivity between the ponds. Ditch blocks would be built in the existing borrow ditches west of the R4 breach to direct tidal flows into the interior of the ponds. Two habitat transition zones would be constructed in R4, approximately 2,500 feet long and 5,100 feet long, with 30:1 slopes and varying steeper slopes at the end transitions. A habitat island would be constructed between R5 and S5 from the remains of the internal levee between these ponds to provide upland wildlife habitat.

Flood Risk Management. To offset the levee breaches in Pond A1 at the Alviso-Mountain View Pond Cluster (Figure 5), the project would raise most of the western levee of A1 and would improve the Coast Casey Forebay levee along the western end of the southern border of A1, raising it and extending it. The improvements would be 1,440 feet long, and 24 feet wide and the design elevation would be 14.7 feet NAVD88. The improvements to the Coast Casey Forebay levee also include excavation to place a shear key, to strengthen the levee. At Ravenswood Pond Cluster (Figure 6), approximately 4,700 feet of improved levee would be constructed on existing levees and would fill in the All-American Canal (AAC). The berm-like levees along both sides of the AAC would be raised and strengthened, and the AAC would be filled in, creating a single levee. Constructing this improved levee would replace the de facto flood risk protection currently provided by the outboard levees on Pond R4. Improvements at the western end of the AAC would extend north along the Ponds R4/R5 border and south along the R3/S5 border to isolate Ponds R5 and S5 from the others so that they can be managed separately.

Public Access and Recreation. At Alviso-Mountain View Pond Cluster (Figure 5), the project would include a public access trail and viewing platform along part of the raised levee along the western side of A1. A Phase 2 trail would be added to the eastern side of A2W with a viewing platform at the north end. At Ravenswood, a Phase 2 trail would be added to the improved levees along the east side of R5 extending south on the east side of S5; a viewing platform would be installed at the junction of the improved levees between R4 and R3 and the east side of R5.

PG&E Infrastructure Improvement. At the Alviso-Mountain View Pond Cluster, the conversion of A2W from pond to tidal marsh would require upgrades to the foundations of sixteen transmission towers due to the introduced tidal flux. In addition, two bridges would be installed to extend over the breaches on the eastern levee of Pond A2W (Figure 5) to provide access to existing PG&E utilities. Existing PG&E access boardwalks would be improved and a new access boardwalk would be constructed along the northern edge of A1, connecting to the existing, improved boardwalk in A2W.  More details on the Project are described in the Environmental Impact Statement/Report, available at: http://www.southbayrestoration.org/planning/phase2/FEISRdownload.html.

Basic Project Purpose: The basic project purpose comprises the fundamental, essential, or irreducible purpose of the project, and is used by USACE to determine whether the project is water dependent. The basic project purpose is to conduct restoration and enhancement activities at former South Bay Salt Ponds, and therefore this project is water-dependent.

Overall Project Purpose: The overall project purpose serves as the basis for the Section 404(b)(1) alternatives analysis, and is determined by further defining the basic project purpose in a manner that more specifically describes the applicant's goals for the project, while allowing a reasonable range of alternatives to be analyzed. The overall project purpose is to: 1) restore and enhance a mix of wetland habitats in the former South Bay salt ponds to address historic losses of tidal marsh habitats and declining ecological values in San Francisco Bay; 2) provide wildlife-oriented public access and recreation, and 3) provide for flood management in the South Bay. Historical losses of approximately 90% of marsh ecosystems around the Bay has led to severe habitat reduction for animal and plant species native to California, including the salt marsh harvest mouse and the California Ridgway’s rail, which are both Federally and state listed as endangered. Public access and recreation elements are important to the overall restoration strategy because of their role in educating the public, achieving regional public access and recreation goals (e.g., for the Bay Trail), and building public support for future restoration.

Project Impacts: Fill discharge into Waters of the US would be required to meet the purpose of the project. Impacts associated with the restoration activities at Alviso-Island Ponds (A19 and A20) include: 600 cubic yards (cy) of fill into 0.22 acres of wetlands and 6,000 cy of fill into 1.00 acre of other waters of the US for installing ditch blocks; 4,000 cy of fill into 0.6 acres of wetlands and 400 cy of fill into 0.10 acre of other waters of the US for ditch blocks associated with widening the breaches of the southern levee; 7,250 cy of fill into 2.35 acres of wetlands and 7,250 cy of fill into 2.35 acres of other waters of the US as side-cast material; dredging impacts include 5,037 cy from 2.00 acres of wetlands and 560 cy from 0.40 acre of other waters of the US for levee lowering and removal, and 1,400 cy from 0.39 acre of wetlands and 190 cy from 0.07 acre of other waters of the US to breach or widen breaches of levees.

Impacts associated with the restoration activities at Alviso-A8 Ponds (A8 and A8S) include: 10,000 cy of fill into 0.91 acre of wetlands and 164,000 cy of fill into 23 acres of other waters of the US to construct habitat transition zones.

Impacts associated with the restoration activities at Alviso-Mountain View Ponds (A1 and A2W) include: 30,120 cy of fill into 6.43 acres of wetlands and 120,480 cy of fill into 25.57 acres of other waters of the US to construct habitat transition zones; 38,280 cy of fill into 5.10 acres of other waters of the US to build eight to ten habitat islands; 17,457 cy of fill into 3.25 acres of wetlands and 34,913 cy of fill into 6.51 acres of other waters of the US to improve levees; dredging impacts include 3,100 cy of fill from 0.65 acre of wetlands to improve levees, and 4,136 cy of fill from .55 acre of wetlands and 1,034 cy of fill from 0.14 acre of other waters of the US to breach levees.

Impacts associated with the restoration activities at Ravenswood Ponds (R3, R4, R5 and S5) include: 7,682 cy of fill into 0.47 acre of wetlands and 38,408 cy of fill into 6.55 acres of other waters of the US for levee improvements; 100 cy of fill into 0.01 acre of wetlands and 900 cy of fill into 0.28 acre of other waters of the US to build ditch blocks; 11,670 cy into 1.32 acres of wetlands and 105,030 cy of fill into 19.03 acres of other waters of the US to construct habitat transition zones; 200 cy of fill into 0.10 acre of wetlands and 200 cy of fill into 0.10 other waters of the US to install water control structures; dredging impacts include 1,000 cy from 0.10 acre of wetlands and 15,000 cy from 4.00 acres of waters of the US to excavate pilot channels; 3,850 cy from 0.89 acre of wetlands and 3,850 cy from 1.10 acres of other waters of the US for levee improvements; 500 cy from 0.08 acre of wetlands and 500 from 0.08 acre of other waters of the US to install water control structures, and 3,533 cy from 0.65 acre of wetlands and 7,067 cy from 1.27 acres of other waters of the US to breach levees.

Impacts associated with required PG&E infrastructure improvements include 12.4 cy of fill into 0.018 acre wetlands and 111.6 cy into 0.162 acre other waters of the US.

Proposed Mitigation: Conservation measures and best management practices are included in the project design to minimize and avoid adverse effects to environmental resources including water quality, sensitive habitats (including wetlands) and wildlife. The project would convert former industrial salt ponds to high quality tidal marsh wetlands (special aquatic sites) and enhanced managed pond habitat. As a result, this project should be considered self-mitigating and no further off-site mitigation will be needed to account for temporary and permanent project impacts.



3. STATE AND LOCAL APPROVALS:

Water Quality Certification: State water quality certification or a waiver is a prerequisite for the issuance of a Department of the Army Permit to conduct any activity which may result in a fill or pollutant discharge into waters of the United States, pursuant to Section 401 of the Clean Water Act of 1972, as amended (33 U.S.C. § 1341 et seq.). The applicant has recently submitted an application to the California Regional Water Quality Control Board (RWQCB) to obtain water quality certification for the project. No Department of the Army Permit will be issued until the applicant obtains the required certification or a waiver of certification. A waiver can be explicit, or it may be presumed, if the RWQCB fails or refuses to act on a complete application for water quality certification within 60 days of receipt, unless the District Engineer determines a shorter or longer period is a reasonable time for the RWQCB to act.

Water quality issues should be directed to the Executive Officer, California Regional Water Quality Control Board, San Francisco Bay Region, 1515 Clay Street, Suite 1400, Oakland, California 94612, by the close of the comment period.

Coastal Zone Management: Section 307(c) of the Coastal Zone Management Act of 1972, as amended (16 U.S.C. § 1456(c) et seq.), requires a Federal applicant seeking a federal license or permit to conduct any activity occurring in or affecting the coastal zone to obtain a Consistency Determination that indicates the activity conforms with the State’s coastal zone management program. Generally, no federal license or permit will be granted until the appropriate State agency has issued a Consistency Determination or has waived its right to do so. Since the project occurs in the coastal zone or may affect coastal zone resources, the applicant is hereby advised to apply for a Consistency Determination from the San Francisco Bay Conservation and Development Commission to comply with this requirement.

Coastal zone management issues should be directed to the Executive Director, San Francisco Bay Conservation and Development Commission, 455 Golden Gate Avenue, Street, Suite 10600, San Francisco, California 94102, by the close of the comment period.

Other Local Approvals: The applicant will be applying for the following additional governmental authorizations for the project: The Applicant will be complying with state and federal laws for protection of endangered species.



4. COMPLIANCE WITH VARIOUS FEDERAL LAWS:

National Environmental Policy Act (NEPA): Upon review of the Department of the Army permit application and other supporting documentation, The USFWS, as the federal lead agency, has prepared an Environmental Impact Statement/Environmental Impact Report for the Project, which is available online at: http://www.southbayrestoration.org/planning/phase2/FEISRdownload.html. At the conclusion of the public comment period, USACE will assess the environmental impacts of the project in accordance with the requirements of the National Environmental Policy Act of 1969 (42 U.S.C. §§ 4321-4347), the Council on Environmental Quality's Regulations at 40 C.F.R. Parts 1500-1508, and USACE Regulations at 33 C.F.R. Part 325. The final NEPA analysis will normally address the direct, indirect, and cumulative impacts that result from regulated activities within the jurisdiction of USACE and other non-regulated activities USACE determines to be within its purview of Federal control and responsibility to justify an expanded scope of analysis for NEPA purposes. The final NEPA analysis will be incorporated in the decision documentation that provides the rationale for issuing or denying a Department of the Army Permit for the project. The final NEPA analysis and supporting documentation will be on file with the San Francisco District, Regulatory Division.

Endangered Species Act (ESA): Section 7(a)(2) of the ESA of 1973, as amended (16 U.S.C. § 1531 et seq.), requires Federal agencies to consult with either the U.S. Fish and Wildlife Service (USFWS) or the National Marine Fisheries Service (NMFS) to ensure actions authorized, funded, or undertaken by the agency are not likely to jeopardize the continued existence of any Federally-listed species or result in the adverse modification of designated critical habitat. As the Federal lead agency for this project, the applicant will be responsible for determining the presence or absence of Federally-listed species and designated critical habitat, and the need to conduct consultation. To complete the administrative record and the decision on whether to issue a Department of the Army Permit for the project, USACE will obtain all necessary supporting documentation from the applicant concerning the consultation process. Any required consultation must be concluded prior to the issuance of a Department of the Army Permit for the project.

Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA): Section 305(b)(2) of the MSFCMA of 1966, as amended (16 U.S.C. § 1801 et seq.), requires Federal agencies to consult with the NMFS on all proposed actions authorized, funded, or undertaken by the agency that may adversely affect essential fish habitat (EFH). EFH is defined as those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity. EFH is designated only for those species managed under a Federal Fisheries Management Plan (FMP), such as the Pacific Groundfish FMP, the Coastal Pelagics FMP, and the Pacific Coast Salmon FMP. As the Federal lead agency for this project, the applicant will be responsible for determining the presence or absence of EFH, and the need to conduct consultation. To complete the administrative record and the decision on whether to issue a Department of the Army Permit for the project, USACE will obtain all necessary supporting documentation from the applicant concerning the consultation process. Any required consultation must be concluded prior to the issuance of a Department of the Army Permit for the project.

Marine Protection, Research, and Sanctuaries Act (MPRSA): Section 302 of the MPRS of 1972, as amended (16 U.S.C. § 1432 et seq.), authorizes the Secretary of Commerce, in part, to designate areas of ocean waters, such as the Cordell Bank, Gulf of the Farallones, and Monterey Bay, as National Marine Sanctuaries for the purpose of preserving or restoring such areas for their conservation, recreational, ecological, or aesthetic values. After such designation, activities in sanctuary waters authorized under other authorities are valid only if the Secretary of Commerce certifies that the activities are consistent with Title III of the Act. No Department of the Army Permit will be issued until the applicant obtains the required certification or permit. The project does not occur in sanctuary waters, and a preliminary review by USACE indicates the project would not likely affect sanctuary resources. This presumption of effect, however, remains subject to a final determination by the Secretary of Commerce, or his designee.

National Historic Preservation Act (NHPA): Section 106 of the NHPA of 1966, as amended (16 U.S.C. § 470 et seq.), requires Federal agencies to consult with the appropriate State Historic Preservation Officer to take into account the effects of their undertakings on historic properties listed in or eligible for listing in the National Register of Historic Places. Section 106 of the Act further requires Federal agencies to consult with the appropriate Tribal Historic Preservation Officer or any Indian tribe to take into account the effects of their undertakings on historic properties, including traditional cultural properties, trust resources, and sacred sites, to which Indian tribes attach historic, religious, and cultural significance. As the Federal lead agency for this project, the applicant will be responsible for determining the presence or absence of historic properties or archaeological resources, and the need to conduct consultation. To complete the administrative record and the decision on whether to issue a Department of the Army Permit for the project, USACE will obtain all necessary supporting documentation from the applicant concerning the consultation process. Any required consultation must be concluded prior to the issuance of a Department of the Army Permit for the project. If unrecorded archaeological resources are discovered during project implementation, those operations affecting such resources will be temporarily suspended until USACE concludes Section 106 consultation with the State Historic Preservation Officer or the Tribal Historic Preservation Officer to take into account any project related impacts to those resources.



5. COMPLIANCE WITH THE SECTION 404(b)(1) GUIDELINES:

Projects resulting in discharges of dredged or fill material into waters of the United States must comply with the Guidelines promulgated by the Administrator of the Environmental Protection Agency under Section 404(b) of the Clean Water Act (33 U.S.C. § 1344(b)). An evaluation pursuant to the Guidelines indicates the project is dependent on location in or proximity to waters of the United States to achieve the basic project purpose. This conclusion raises the (rebuttable) presumption of the availability of a practicable alternative to the project that would result in less adverse impact to the aquatic ecosystem, while not causing other major adverse environmental consequences. The applicant has submitted an analysis of project alternatives which is being reviewed by USACE.



6. PUBLIC INTEREST EVALUATION:

The decision on whether to issue a Department of the Army Permit will be based on an evaluation of the probable impacts, including cumulative impacts, of the project and its intended use on the public interest. Evaluation of the probable impacts requires a careful weighing of the public interest factors relevant in each particular case. The benefits that may accrue from the project must be balanced against any reasonably foreseeable detriments of project implementation. The decision on permit issuance will, therefore, reflect the national concern for both protection and utilization of important resources. Public interest factors which may be relevant to the decision process include conservation, economics, aesthetics, general environmental concerns, wetlands, cultural values, fish and wildlife values, flood hazards, floodplain values, land use, navigation, shore erosion and accretion, recreation, water supply and conservation, water quality, energy needs, safety, food and fiber production, mineral needs, considerations of property ownership, and, in general, the needs and welfare of the people.



7. CONSIDERATION OF COMMENTS:

USACE is soliciting comments from the public; Federal, State and local agencies and officials; Native American Nations or other tribal governments; and other interested parties in order to consider and evaluate the impacts of the project. All comments received by USACE will be considered in the decision on whether to issue, modify, condition, or deny a Department of the Army Permit for the project. To make this decision, comments are used to assess impacts on endangered species, historic properties, water quality, and other environmental or public interest factors addressed in a final environmental assessment or environmental impact statement. Comments are also used to determine the need for a public hearing and to determine the overall public interest of the project.



8. SUBMITTING COMMENTS:

During the specified comment period, interested parties may submit written comments to Frances Malamud-Roam, San Francisco District, Regulatory Division, 1455 Market Street, 16th Floor, San Francisco, California 94103-1398; comment letters should cite the project name, applicant name, and public notice number to facilitate review by the Regulatory Permit Manager. Comments may include a request for a public hearing on the project prior to a determination on the Department of the Army permit application; such requests shall state, with particularity, the reasons for holding a public hearing. All substantive comments will be forwarded to the applicant for resolution or rebuttal. Additional project information or details on any subsequent project modifications of a minor nature may be obtained from the applicant and/or agent, or by contacting the Regulatory Permit Manager by telephone or e-mail cited in the public notice letterhead. An electronic version of this public notice may be viewed under the Public Notices tab on the USACE website: http://www.spn.usace.army.mil/Missions/Regulatory.