SECTION 3.4 BIOLOGICAL RESOURCES 3.4- BIOLOGICAL RESOURCES 3.4 BIOLOGICAL RESOURCES This section discusses the existing sensitive biological resources of the San Francisco Bay Estuary (the Estuary) that could be affected by project-related construction and locally increased levels of boating use, identifies potential impacts to those resources, and recommends mitigation strategies to reduce or eliminate those impacts. The Initial Study for this project identified potentially significant impacts on shorebirds and rafting waterbirds, marine mammals (harbor seals), and wetlands habitats and species. The potential for spread of invasive species also was identified as a possible impact. 3.4.1 BIOLOGICAL RESOURCES SETTING HABITATS WITHIN AND AROUND SAN FRANCISCO ESTUARY The vegetation and wildlife of bayland environments varies among geographic subregions in the bay (Figure 3.4-1), and also with the predominant land uses: urban (commercial, residential, industrial/port), urban/wildland interface, rural, and agricultural. For the purposes of discussion of biological resources, the Estuary is divided into Suisun Bay, San Pablo Bay, Central San Francisco Bay, and South San Francisco Bay (See Figure 3.4-2). The general landscape structure of the Estuary’s vegetation and habitats within the geographic scope of the WT is described below. URBAN SHORELINES Urban shorelines in the San Francisco Estuary are generally formed by artificial fill and structures armored with revetments, seawalls, rip-rap, pilings, and other structures. Waterways and embayments adjacent to urban shores are often dredged. With some important exceptions, tidal wetland vegetation and habitats adjacent to urban shores are often formed on steep slopes, and are relatively recently formed (historic infilled sediment) in narrow strips. They are usually dominated by relatively few widespread and common marsh species, with a high proportion of non-native marsh species. Special- status plant species, with a few important exceptions, are usually absent in urban shores. On the terrestrial side of urban shorelines, natural or native vegetation is generally lacking or minimal. Non-native terrestrial vegetation (especially annual grasses, broadleaf weeds, and escaped or planted non-native ornamental trees and shrubs) is prevalent along most urban shores of commercial developments, ports, frontage roads, former military bases, and industrial sites. The matrix of intensive urban land use and infrastructure in much of Central San Francisco Bay tends to override natural or potential geographic variation in vegetation and habitats of adjacent baylands and shore vegetation. Exceptions occur where significant erratic patches of natural or restored native shore vegetation are included within entirely urbanized landscapes, such as Arrowhead Marsh in San Leandro Bay, Crown Beach/Elsie Roemer Marsh in Alameda, or Crissy Field in San Francisco. In the northern Estuary (San Pablo Bay and eastward), the relation between intensive urban land use and open space is usually reversed: intensive urban land uses more often occur within a matrix of open space and wildland vegetation, where more sensitive native vegetation and habitats co-occur with urban development. The density of Backbone Sites is relatively high in the urban landscape setting. SF BAY AREA WATER TRAIL PLAN 3.4-1 COASTAL CONSERVANCY DRAFT EIR JUNE 2008 3.4- BIOLOGICAL RESOURCES URBAN/WILDLAND INTERFACES Urban (or suburban) development along the shores of the Estuary is extensive, and often occurs adjacent to large blocks of wetland habitats within regional parks, wildlife refuges, ecological reserves owned and managed by state or municipal agencies. This matrix of urban/wildland interface prevails in shorelines of South San Francisco Bay, most of Marin County along Central San Francisco Bay and San Pablo Bay, around expanding cities in San Pablo Bay along the northern Contra Costa shoreline, and northern Suisun Marsh. Large, continuous blocks of native vegetation and habitats, often including old and species-rich remnants, are close to urban shorelines in these conditions. This proximity increases the potential exposure of sensitive tidal wetland habitats to non-motorized recreational boating, or other impacts emanating from trailheads. The proximity of source populations of sensitive species to urban areas also increases the potential for sensitive species to establish opportunistically in urban shorelines. For example, some sensitive plant populations occur adjacent to residential, commercial, and industrial or military port/marina developments along shorelines in Vallejo, Fairfield, Concord, San Rafael, and Richardson Bay. The density of Backbone Sites is relatively high in the urban/wildland setting. If urban land uses continue to spread into former agricultural or rural areas, the urban/wildland interface is expected to increase in the Bay Area. RURAL AND AGRICULTURAL HABITATS Large blocks of ecologically important wetland and adjacent upland habitats are most likely to occur in rural and agricultural settings of the San Francisco Estuary, where travel distances to major urban populations are longest. True undeveloped open spaces (i.e., original soils intact) along the bay edge are largely confined to San Pablo Bay and the vicinity of Suisun Marsh. The entire matrix of the landscape is likely to support at least remnants of the original pre-reclamation biological diversity of native habitats. The density of Backbone Sites is relatively low in the rural and agricultural landscape setting of San Pablo Bay and Suisun Marsh. OPEN WATER HABITATS Open water habitats within San Francisco Estuary are classified by the Goals Project into two categories: shallow bay (subtidal areas above 18 foot depth below Mean Lower Low Water or MLLW1), and deep bay (subtidal channels deeper than 18 feet below MLLW). The Estuary currently contains almost 172,000 acres of shallow bay/channel habitat, and more than 82,000 acres of deep bay/channel habitat (Goals Project 1999). Primarily unvegetated soft bottom sediments (bay muds and sand deposits) lie underneath most shallow and deep-water habitats, but some shallow bay habitats contain stands of eelgrass (Zostera marina), which serve as valuable habitat for a wide range of fish and invertebrates. Eelgrass beds are also associated with uncommon nearshore areas with 1 Lower low water is the lower of the two low waters of any tidal day. Mean lower low water is the average height of the lower low waters over a 19-year period. For shorter periods of observation, corrections are applied to eliminate known variations and reduce the result to the equivalent of a mean 19-year value. SF BAY AREA WATER TRAIL PLAN 3.4-4 COASTAL CONSERVANCY DRAFT EIR JUNE 2008 3.4- BIOLOGICAL RESOURCES coarser sediment, or rocky substrates infilled with mud or sand. The restoration of eelgrass habitats is currently the focus of multiple research and implementation efforts throughout the Bay. Other shallow bay areas, such as locations near Point San Quentin, are similar focal areas for the restoration of native oyster bed, which have largely disappeared from the Estuary. BIOLOGICAL RESOURCES IN SAN FRANCISCO ESTUARY VEGETATION Vegetation refers to the overall plant cover of a habitat, including its structural and other physical features, in addition to the species composition. Vegetation provides value for wildlife habitat (cover, food resources), physical ecological functions (sediment trapping, erosion buffering), chemical ecological functions (biogeochemical soil processes: sequestering or cycling carbon, mineral nutrients, contaminants), or inherent biological diversity (rare plant species or biologically important genetic variation among populations). Important biological diversity of plants may occur at the level of population (genetic variation), species (rare plant conservation), and community (e.g., relatively intact or natural vegetation stands). Some plants can also have negative public resource values, particularly invasive non-native noxious weeds of wetlands and terrestrial habitats. There is substantial regional variation in the vegetation of tidal and non-tidal baylands in the San Francisco Estuary (Baye et al. 2000). WT sites may be located near areas ranging from only sparse or weedy non-native vegetation with limited habitat function, to extensive marshes with well-developed, mature native marsh vegetation. In addition, different types of marshes and shoreline vegetation in different parts of the Estuary support different plant and wildlife species (including special-status species). Geographic variation in vegetation and habitats provides an important context for evaluating potential WT impacts to special-status plant and wildlife species, and wetlands. Major bayland vegetation communities and habitats are summarized below. Bayland habitats are indicated on Figure 3.4-1. Tidal Salt Marsh Tidal salt marshes are jurisdictional (state- and federally regulated) wetlands (see Section 3.4.2). They are distributed primarily around San Francisco Bay and the inner margins of San Pablo Bay. They are characterized by prevalence of native marsh plants that can tolerate wetland soil salinity that frequently approaches marine salinity (34 parts per thousand salt) during the growing season. Most modern salt marshes in the Estuary are generally dominated by relatively few native plant species, such as pickleweed (Sarcocornia pacifica), saltgrass (Distichlis spicata), fleshy jaumea (Jaumea carnosa), and sometimes large summer