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Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region

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Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region July 2009 Executive Summary Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region Pursuant to section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act of 1976 (16 U.S.C. §1855(b)), the United States Army Corps of Engineers (USACE) and the United States Environmental Protection Agency (USEPA), as the federal lead and co-lead agencies, respectively, submit this Programmatic Essential Fish Habitat (EFH) Assessment for the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region. This document provides an assessment of the potential effects of the on-going dredging and dredged material placement activities of all federal and non-federal maintenance dredging projects in the action area (see Figure 1.1 located on page 3). The SF Bay LTMS program area spans 11 counties, including: Marin, Sonoma, Napa, Solano, Sacramento, San Joaquin, Contra Costa, Alameda, Santa Clara, San Mateo and San Francisco counties. It does not include the mountainous or inland areas far removed from navigable waters. The geographic scope of potential impacts included in this consultation (action area) comprises the estuarine waters of the San Francisco Bay region, portions of the Sacramento-San Joaquin Delta (Delta) west of Sherman Island and the western portion of the Port of Sacramento and Port of Stockton deep water ship channels. It also includes the wetlands and shallow intertidal areas that form a margin around the Estuary and the tidal portions of its tributaries. Lastly, it includes the San Francisco Deep Ocean Disposal Site (SF-DODS), the San Francisco Bar Channel Disposal Site (SF-8) and the nearshore zone off Ocean Beach, as well as the waters that are used by vessels en route to these sites. Within the action area, there are at least 13 federal (maintained by USACE), 105 non- federal maintenance dredging projects, four in-Bay disposal sites (SF-9, SF-10, SF-11 and SF-16), two ocean disposal sites SF-8 and SF-DODS, several beneficial use wetland restoration sites (the on-going Hamilton Wetland Restoration Project, Montezuma Wetlands and Bair Island), and privately-used beneficial use and upland sites. The San Francisco Bay Long Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region (SF Bay LTMS) was formed in the early 1990s in response to the public’s growing concern over the potential direct, indirect and cumulative effects of dredging and dredged material disposal activities on the already stressed resources of the San Francisco Bay/Estuary (Bay or Estuary). The 50-year SF Bay LTMS program is comprised of state and federal regulatory agencies with primary authority to review and permit dredging and dredged material disposal activities in the San Francisco Bay area. Partnering agencies include: United States Army Corps of Engineers (USACE), United States Environmental Protection Agency (USEPA), San 1 Francisco Bay Regional Water Resources Control Board (SFBRWRCB), State Water Resources Control Board (SWRCB), San Francisco Bay Conservation and Development Commission (BCDC) and State Lands Commission (SLC). Formal implementation of the SF Bay LTMS began in 2001 with the adoption of the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region Management Plan (LTMS Management Plan). The LTMS Management Plan was proceeded by an extensive eight-year federal and state planning effort which culminated in the Long-Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region Final Environmental Impact Statement/Environmental Impact Report (EIS/EIR), finalized in October 1998. The SF Bay LTMS EIS/EIR and subsequent Management Plan called for reversing the historic practice of disposing 80 percent or more of all material dredged from the Estuary at in- Bay disposal sites and requires that at least 80 percent of all dredged material be placed at beneficial use sites, upland or at ocean disposal sites, with only limited volumes of material being placed at in-Bay disposal sites. Over the life of the SF Bay LTMS, the selected alternative aims to: • Maintain in an economically and environmentally sound manner those channels necessary for navigation in San Francisco Bay and eliminate unnecessary dredging activities. • Conduct dredged material disposal in the most environmentally sound manner. • Maximize the use of dredged material as a resource. • Maintain the cooperative permitting framework for dredging and disposal applications. Prior to implementation of the SF Bay LTMS, an average of 6.0 million cubic yards of material dredged from the Estuary was placed back in Estuary at four in-Bay disposal sites. Since the SF Bay LTMS Management Plan was implemented in 2001, allowable in-Bay disposal has significantly decreased: from pre-LTMS quantities of over 6.0 million cubic yards per year to current quantities of less than 2.0 million cubic yards per year. Additionally, reductions will automatically occur in 2010 and 2013, until the final in-Bay disposal limit of 1.25 million cubic yards per year is reached. The reduction of in- Bay disposal to date is remarkable; but, even more important is the SF Bay LTMS goal to increase beneficial use of dredged material. Beneficial use of dredged material has been a success in restoring several important wetland ecosystems surrounding the Estuary, including Sonoma Baylands, Montezuma Wetlands, and the ongoing Hamilton Wetlands Restoration Project. These three projects alone total approximately 3,000 acres of restored and enhanced habitat that benefits all fish and wildlife species that depend on the Estuary. Further, these restoration sites provide a dredged material beneficial use capacity of approximately 27.5 million cubic yards. Other smaller beneficial use projects are currently being constructed and the SF Bay LTMS continues to look for beneficial use opportunities. At times, beneficial use is not possible. When this occurs, rather than being disposed of in the Estuary, some dredged material is diverted to the environmentally superior SF- 2 DODS site. Since the 1995 designation of SF-DODS as a deep open ocean aquatic disposal site, approximately 15 million cubic yards of dredged material has been disposed there. This has significantly reduced and eliminated some of the effects of aquatic dredged material disposal on the Estuary’s water and sediment quality, as well as direct effects (e.g., burial, abrasion, adhesion of particles to eggs) and indirect effects (e.g., ingestion of constituents of concern, bioaccumulation, reduced fitness) of disposal and subsequent increases in suspended sediment concentrations on aquatic organisms. Most of the effects of dredging and dredging material placement are temporary and localized and, with the exception of impacts associated with a changed bottom topography (potential changes in local hydrodynamics and in the makeup of the benthic resources present in the dredged area), the impacts end when dredging ends. The most substantial impacts tend to be on water quality – the potential for resuspension of constituents of concern buried in the sediments – and the impacts on biological resources in the dredged and dredged material disposal areas. Although there are adverse impacts associated with dredging and dredged material disposal, as presented in Section 8.0 of the attached EFH Assessment and summarized in Table 1.0 (below), it is clear that the SF Bay LTMS has brought about major improvements in the management of dredging and dredged material disposal in the San Francisco Bay area. These improvements have directly benefited EFH and EFH- managed species, as well as the overall ecosystem of the Estuary. Not only is the SF Bay LTMS directly responsible for improving the management of dredging and dredged material disposal; they are responsible for several other accomplishments that directly and indirectly benefit EFH, EFH-managed species and the Estuary, including: • Expansion of the Hamilton Wetlands Restoration Project with the Bel Marin Keys “Unit V” property will increase established tidal wetlands restoration capacity to approximately 5,000 acres and 45 million cubic yards of dredged material. • Subtidal aquatic habitat was enhanced in Oakland Middle Harbor through beneficial use of approximately 6 million cubic yards of dredged material. • The Montezuma Project can accept some contaminated dredged material for capping and, therefore, removes some constituents of concern from the Estuary while also restoring habitat. • A variety of other small or private beneficial use projects have occurred in the last several years. • Environmental work windows for dredging and dredged material disposal activities were established to reduce the potential adverse effects on sensitive species. With assistance from NOAA-Fisheries, USFWS and California Department of Fish and Game, advanced planning has significantly reduced the amount of dredging conducted outside of the environmental work windows. In 2008, the inter-agency advanced planning resulted in only 10 percent of all Bay area dredging being conducted outside the environmental work windows. • Environmental work windows continue to be refined through SF Bay LTMS funded studies, such as the Juvenile
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