4.3 Delta Fisheries and Aquatic Resources (PDF)
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4.3 Delta Fisheries and Aquatic Resources 4.3 Delta Fisheries and Aquatic Resources This section describes the existing fishery and aquatic habitat conditions within the Bay-Delta estuary that would potentially be affected by the Los Vaqueros Reservoir Expansion Project, presents the applicable regulatory background, provides an assessment of potential fisheries and aquatic resources effects, and, where appropriate, identifies suitable mitigation to reduce potentially significant impacts to a less-than-significant level. 4.3.1 Affected Environment Regulatory Setting Federal Federal Endangered Species Act Under the Federal Endangered Species Act (FESA), the Secretary of the Interior and the Secretary of Commerce have joint authority to list a species as threatened or endangered (United States Code [USC], Title 16, Section 1533[c]). FESA prohibits the “take” of endangered or threatened fish and wildlife species, the take of endangered or threatened plants in areas under federal jurisdiction or in violation of state law, or adverse modifications to their critical habitat. Under FESA, the definition of “take” is to “harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct.” The U.S. Fish and Wildlife Service (USFWS) and National Oceanic and Atmospheric Administration/National Marine Fisheries Service (NMFS) also interpret the definition of “harm” to include significant habitat modification that could result in the take of a species. If an activity would result in the take of a federally listed species, one of the following is required: an incidental take permit under Section 10(a) of FESA, or an incidental take statement issued pursuant to federal interagency consultation under Section 7 of FESA. Such authorization typically requires various measures to avoid and minimize species take, and to protect the species and avoid jeopardy to the species’ continued existence. Pursuant to the requirements of Section 7 of FESA, a federal agency reviewing a proposed project which it may authorize, fund, or carry out must determine whether any federally listed threatened or endangered species, or species proposed for federal listing, may be present in the project area and determine whether implementation of the proposed project is likely to affect the species. In addition, the federal agency is required to determine whether a proposed project is likely to jeopardize the continued existence of a listed species or any species proposed to be listed under FESA or result in the destruction or adverse modification of critical habitat proposed or designated for such species (16 USC 1536[3], [4]). NMFS administers FESA for marine fish species, including anadromous salmonids such as Central Valley steelhead, winter-run and spring-run chinook salmon, and green sturgeon. USFWS administers FESA for non-anadromous and non-marine fish species such as delta smelt Los Vaqueros Reservoir Expansion Project 4.3-1 February 2009 Draft EIS/EIR Los Vaqueros Reservoir Expansion Project (and longfin smelt, which has been recently proposed for listing). Projects for which a federally listed species is present and likely to be affected by an existing or proposed project must receive authorization from USFWS and/or NMFS. Authorization may involve a letter of concurrence that the project will not result in the potential take of a listed species, or may result in the issuance of a Biological Opinion (BO) that describes measures that must be undertaken to minimize the likelihood of an incidental take of a listed species. A project that is determined by NMFS or USFWS to jeopardize the continued existence of a listed species cannot be approved under a BO. Where a federal agency is not authorizing, funding, or carrying out a project, take that is incidental to the lawful operation of a project may be permitted pursuant to Section 10(a) of FESA through approval of a habitat conservation plan (HCP). FESA requires the federal government to designate “critical habitat” for any species it lists under the Endangered Species Act. “Critical habitat” is defined as: (1) specific areas within the geographical area occupied by the species at the time of listing, if they contain physical or biological features essential to the species conservation, and those features that may require special management considerations or protection; and (2) specific areas outside the geographical area occupied by the species if the agency determines that the area itself is essential for conservation. Implementation of the State Water Project (SWP) and Central Valley Project (CVP) coordinated Operations Criteria and Plan (OCAP), under which the U.S. Department of the Interior, Bureau of Reclamation, Mid-Pacific Region (Reclamation) and California Department of Water Resources (DWR) jointly manage dam releases to the Delta and exports from the Delta, is a key factor affecting hydrology and aquatic habitat conditions within the Bay-Delta estuary. This is described in Chapter 2 and Appendix C-3. Magnuson-Stevens Fishery Conservation and Management Act – Essential Fish Habitat The Pacific Fishery Management Council (PFMC) has designated the Delta, San Francisco Bay, and Suisun Bay as Essential Fish Habitat (EFH) to protect and enhance habitat for coastal marine fish and macroinvertebrate species that support commercial fisheries such as Pacific salmon. The amended Magnuson-Stevens Fishery Conservation and Management Act, also known as the Sustainable Fisheries Act (Public Law 104-297), requires that all federal agencies consult with NMFS on activities or proposed activities authorized, funded, or undertaken by that agency that may adversely affect EFH of commercially managed marine and anadromous fish species. As part of the OCAP Biological Assessment, Reclamation and DWR have addressed anticipated effects of SWP and CVP operations on EFH within the Bay-Delta estuary for use in the reconsultation for compliance with the Act. The EFH provisions of the Sustainable Fisheries Act are designed to protect fishery habitat from being lost due to disturbance and degradation. The Act requires that EFH must be identified for all species federally managed by the PFMC, which is responsible for managing commercial fishery resources along the coasts of Washington, Los Vaqueros Reservoir Expansion Project 4.3-2 February 2009 Draft EIS/EIR 4.3 Delta Fisheries and Aquatic Resources Oregon, and California. Three fishery management plans cover species that occur in the project area, and designate EFH within the entire Bay-Delta estuary: • Pacific Groundfish Fishery Management Plan: starry flounder • Coastal Pelagic Fishery Management Plan: northern anchovy and Pacific sardine • Pacific Salmon Fishery Management Plan: chinook salmon Clean Water Act The U.S. Army Corps of Engineers (USACE) administers a number of laws and programs designed to protect fish and wildlife resources. Principal of these, with respect to the project alternatives, is Section 404 of the Clean Water Act. Section 404 regulates activities in wetlands and “other waters of the United States.” Wetlands are a subset of waters of the U.S., which are defined in the Code of Federal Regulations (33 CFR 328.3[a]; 40 CFR 230.3[s]) as: 1. All waters that are currently used, were used in the past, or may be susceptible to use in interstate or foreign commerce, including all waters that are subject to the ebb and flow of the tide 2. All interstate waters including interstate wetlands. Wetlands are defined by the federal government [33 CFR 328.3(b), 1991] as those areas that are inundated or saturated by surface or groundwater at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions 3. All other waters such as intrastate lakes, rivers, streams (including intermittent streams), mud flats, sand flats, wetlands, sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds, the use, degradation, or destruction of which could affect interstate or foreign commerce including any such waters • Which are or could be used by interstate or foreign travelers for recreational or other purposes; or • From which fish or shellfish are or could be taken and sold in interstate or foreign commerce; or • Which are used or could be used for industrial purposes by industries in interstate commerce. 4. All impoundments of waters otherwise defined as waters of the United States under the definition 5. Tributaries of waters identified in paragraphs (1) through (4) 6. The territorial sea 7. Wetlands adjacent to waters identified in paragraphs (1) through (6) Los Vaqueros Reservoir Expansion Project 4.3-3 February 2009 Draft EIS/EIR Los Vaqueros Reservoir Expansion Project State California Endangered Species Act Pursuant to the California Endangered Species Act (CESA) and Section 2081 of the California Fish and Game Code, a permit from the California Department of Fish and Game (CDFG) is required for activities that could result in the take of a state-listed threatened or endangered species (i.e., species listed under CESA). The definition of “take” is to hunt, pursue, catch, capture, or kill, or attempt to hunt, pursue, catch, capture, or kill (Fish and Game Code Section 86). The state definition does not include “harm” or “harass,” as the federal definition does. As a result, the threshold for take under CESA is typically higher than that under FESA. Section 2080 of the Fish and Game Code prohibits