Federal Requirements
Endangered Species Act
Section 7 of the ESA requires federal agencies, in consultation with USFWS and/or NOAA Fisheries, to ensure that their actions do not jeopardize the continued existence of endangered or threatened species or result in the destruction or adverse modification of the critical habitat of these species. The required steps in the Section 7 consultation process are as follows.

• Agencies must request information from USFWS and/or NOAA Fisheries on the existence in a project area of listed species or species proposed for listing.

• Following receipt of the USFWS/NOAA Fisheries response to this request, agencies generally prepare a BA to determine whether any listed species or species proposed for listing are likely to be affected by a proposed action.

• Agencies must initiate formal consultation with USFWS and/or NOAA Fisheries if the proposed action might adversely affect listed species.

• USFWS and/or NOAA Fisheries must prepare a BO to determine whether the action would jeopardize the continued existence of listed species or adversely modify their critical habitat.

• If a finding of jeopardy or adverse modifications is made in the BO, USFWS and/or NOAA Fisheries must recommend reasonable and prudent alternatives that would avoid jeopardy, and the federal agency must modify the project to ensure that listed species are not jeopardized and that their critical habitat is not adversely modified (unless an exemption from this requirement is granted).

In the preparation of the SDIP EIR/EIS, the MSCS approach was used and an ASIP, serving as the equivalent to the CALFED Programmatic SDIP BA, has been prepared in compliance with Section 7 of the ESA.

Clean Water Act Section 404(b)(1) Guidelines and Section 401 Section 404.
Section 404 of the CWA requires that a permit be obtained from the Corps for the discharge of dredged or fill material into “waters of the United States, including wetlands.” Waters of the United States include wetlands and lakes, rivers, streams, and their tributaries. Wetlands are defined for regulatory purposes, at 33 CFR 328.3 and 40 CFR 230.3, as areas inundated or saturated by surface water 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.

CWA Section 404(b) requires that the Corps issue permits in compliance with guidelines developed by EPA. These guidelines require that there be a demonstration that no alternative is available to meet the project purpose and need that does not result in a discharge of fill in waters. Once this first test has been satisfied, the project that is permitted must be the least environmentally damaging practical alternative before the Corps may issue a permit for the proposed activity.

Actions typically subject to Section 404 requirements are those that would take place in wetlands or stream channels that convey natural runoff, including intermittent streams, even if they have been realigned. Artificial channels that convey only irrigation water usually are not included, unless they connect directly to jurisdictional waters of the United States. Within stream channels, a permit under Section 404 would be needed for any discharge activity below the ordinary high-water mark, which is the line on the shore established by the fluctuations of water and indicated by physical characteristics such as a clear, natural line impressed on the bank, shelving, changes in the character of soil, destruction of terrestrial vegetation, or the presence of litter or debris.

The Programmatic ROD for the CALFED Final Programmatic EIS/EIR includes a CWA Section 404 MOU signed by Reclamation, EPA, the Corps, and DWR. Under the terms of the MOU, when a project proponent applies for a Section 404 individual permit for CALFED projects, the proponent is not required to reexamine program alternatives already analyzed in the Programmatic EIS/EIR. The Corps and EPA will focus on project-level alternatives that are consistent with the Programmatic EIS/EIR when they select the least environmentally damaging practicable alternative at the time of a Section 404 permit decision.

Note: Section 404 jurisdiction encompasses areas regulated by Section 10; the Corps typically combines the permit requirements of Section 10 and Section 404 into one permitting process.

Section 401. Under CWA Section 401, applicants for a federal license or permit to conduct activities that may result in the discharge of a pollutant into waters of the United States must obtain certification from the state in which the discharge would originate or, if appropriate, from the interstate water pollution control agency with jurisdiction over affected waters at the point where the discharge would originate. Therefore, all projects that have a federal component and may affect state water quality (including projects that require federal agency approval [such as issuance of a Section 404 permit]) must also comply with CWA Section 401. In California, the authority to grant water quality certification has been delegated to the SWRCB, and applications for water quality certification under CWA Section 401 are typically processed by the RWQCB with local jurisdiction. Water quality certification requires evaluation of potential impacts in light of water quality standards and CWA Section 404 criteria governing discharge of dredged and fill materials into waters of the United States.

For purposes of this project, Reclamation will obtain certification from the Central Valley RWQCB under Section 401 of the CWA.

River and Harbors Appropriation Act of 1899
The River and Harbors Appropriation Act of 1899 addresses activities that involve the construction of dams, bridges, dikes, and other structures across any navigable water. Placing obstructions to navigation outside established federal lines and excavating from or depositing material in such waters require permits from the Corps. In the Corps Sacramento District, navigable waters of the United States in the project area that are subject to the requirements of the River and Harbors Appropriation Act are Middle River, San Joaquin River, Old River, and all waterways in the Sacramento–San Joaquin drainage basin affected by tidal action (U.S. Army Corps of Engineers 2003). Sections of the River and Harbors Act applicable to the SDIP are described below.

Section 9. Section 9 (33 USC 401) prohibits the construction of any dam or dike across any navigable water of the United States in the absence of Congressional consent and approval of the plans by the Chief of Engineers and the Secretary of the Army. Where the navigable portions of the water body lie wholly within the limits of a single state, the structure may be built under authority of the legislature of that state, if the location and plans or any modification thereof are approved by the Chief of Engineers and the Secretary of the Army.

Section 10. Section 10 (33 USC 403) prohibits the unauthorized obstruction or alteration of any navigable water of the United States. This section provides that the construction of any structure in or over any navigable water of the United States, or the accomplishment of any other work affecting the course, location, condition, or physical capacity of such waters, is unlawful unless the work has been recommended and authorized by the Chief of Engineers.

Executive Order 11990 (Protection of Wetlands)
Executive Order 11990 (May 24, 1977) requires federal agencies to prepare wetland assessments for proposed actions located in or affecting wetlands. Agencies must avoid undertaking new construction in wetlands unless no practicable alternative is available and the proposed action includes all practicable measures to minimize harm to wetlands. This chapter of the EIS/EIR describes impacts on wetlands and mitigation measures for reducing significant impacts.

State Requirements
California Endangered Species Act
CESA requires a state lead agency to consult formally with DFG when a proposed action may affect state-listed endangered or threatened species. The provisions of the ESA and CESA will often be activated simultaneously. The assessment of project effects on species listed under both the ESA and CESA is addressed in USFWS’s and NOAA Fisheries’ BOs. However, for those species listed only under CESA, DWR must formally consult with DFG, and DFG must issue a BO separate from USFWS’s BO.

California State Wetlands Conservation Policy
The Governor of California issued an executive order on August 23, 1993, that created a California State Wetlands Conservation Policy. This policy is being implemented by an interagency task force that is jointly headed by the State Resources Agency and the California Environmental Protection Agency (Cal-EPA). The policy’s three goals are to (Cylinder et al. 1995):

1. ensure no overall net loss and a long-term net gain in wetlands acreage and values in a manner that fosters creativity, stewardship, and respect for private property;

2. reduce the procedural complexity of state and federal wetland conservation program administration; and

3. encourage partnerships that make restoration, landowner incentives, and cooperative planning the primary focus of wetlands conservation.

State Regional Water Quality Control Board
Water Code Section 13260 requires “any person discharging waste, or proposing to discharge waste, in any region that could affect the waters of the state to file a report of discharge (an application for waste discharge requirements).” Under the Porter-Cologne definition, the term waters of the state is defined as “any surface water or groundwater, including saline waters, within the boundaries of the state.” Although all waters of the United States that are within the borders of California are also waters of the state, the converse is not true (i.e., in California, waters of the United States represent a subset of waters of the state). Thus, California retains authority to regulate discharges of waste into any waters of the state, regardless of whether the Corps has concurrent jurisdiction under Section 404.

Section 1602 of the California Fish and Game Code
DFG regulates work that will substantially affect resources associated with rivers, streams, and lakes in California, pursuant to Fish and Game Code Sections 1600–1607. Any action from a public project that substantially diverts or obstructs the natural flow or changes the bed, channel, or bank of any river, stream, or lake or uses material from a streambed must be previously authorized by DFG in a Lake or Streambed Alteration Agreement under Section 1602 of the Fish and Game Code. This requirement may, in some cases, apply to any work undertaken within the 100-year floodplain of a body of water or its tributaries, including intermittent streams and desert washes. As a general rule, however, it applies to any work done within the annual high-water mark of a wash, stream, or lake that contains or once contained fish and wildlife or that supports or once supported riparian vegetation.

Activities associated with the SDIP that require Section 1602 authorization and a Streambed Alteration Agreement include the modification and setting back of existing levees, placement of fish and flow control barriers, and conveyance improvements. These actions would result in the alteration of the flow within water bodies and occur within the annual high-water mark of water bodies that contain wildlife and support riparian vegetation.

The current temporary barriers program operates under DFG Section 1602 authorization. This EIS/EIR will be used as the CEQA review document by DWR as part of a new permit application, submitted to DFG for either continued authorization of activities under the existing agreement or for the issuance of a new Streambed Alteration Agreement (California Fish and Game Code 1600 et seq.).