The CVBDB's mission is to gather and provide information and recommendations that will permit others (such as other units of the DFG and other agencies such as the federal Environmental Protection Agency (EPA) , the U.S. Fish and Wildlife Service (USFWS), the U.S. Bureau of Reclamation (USBR), the State Water Resources Control Board (SWRCB), and the California Department of Water Resources (DWR)) to develop procedures, policies and regulations that will protect the flora and fauna of the bay, Delta and adjoining tributary environments from harm, and that will enhance the survival of those species that are listed as rare, threatened or endangered.

These recommendations are made in an atmosphere of competing interests for scarce resources from a variety of public and private sources. Water and other estuary resources are in demand by rural agriculture, cities, anglers, developers, environmentalists, and others. To provide a means of resolving demands while protecting species and habitat, a variety of federal and state laws, policies and regulations have been enacted. Federal and state laws mandate restrictions, and regulations relative to listed species, water policies, land development practices and other environmental and toxic issues.

Many federal and state agencies have established jurisdictions regarding specific water and resource policies and regulations. In support of their jurisdictions, they carry out a variety of research and analyses. In order to promote cost effective, non-overlapping, cooperative research, an Interagency Ecological Program (IEP) has been established by federal Memorandum of Understanding (MOU) between the member agencies. The IEP sets research priorities and funds specific programs in support of agency program mandates. The CVBDB chairs the IEP and receives contract funds from the agencies, apportioned by the IEP. The interagency MOU requires all CVBDB's project data to be stored in a common electronic format and to be available for access by the other IEP agencies and by the public.

The state constitution gives the SWRCB regulatory jurisdiction over California's water resources, including establishment and adjudication of water rights. The SWRCB's Water Right Decision 1485 requires that most of the proposed and ongoing projects affecting the waters and ecosystems of the Sacramento-San Joaquin Delta and Suisun Marsh be reviewed and approved by the SWRCB. The SWRCB requires biological and environmental studies be carried out by DWR and USBR to show possible and ongoing effects of their projects and to provide analysis and plans for mitigating or eliminating any adverse effects upon the ecosystem, including the fisheries. For example Decision 1485 states in part that the permittees (DWR and USBR) "Conduct ongoing and future monitoring surveys as recommended by California Department of Fish and Game and concurred in by the Board concerning food chain relationships and fisheries impacts as they are affected by CVP and SWP operations in the Delta and Suisun Marsh."

Decision 1485 goes on to require that the "Permittees shall make available to the Board and other interested agencies upon request results of the above monitoring as soon as practicable following the month during which the monitoring was accomplished. Annual reports summarizing the previous calendar year's findings and detailing future study plans shall be submitted to the Board by January 15 of each year. Detailed reports containing the previous year's monitoring results shall be submitted by August 1 of each year." To support these requirements, DWR and USBR contract this work to the DFG's Central Valley Bay-Delta Branch. By contract, the CVBDB is required to support the SWRCB's research, monitoring and reporting requirements. Ninety percent of the CVBDB's project work/PY funding is derived from contracts with DWR, USBR, and to a lesser extent other agencies.

In addition to D-1485 and the interagency MOU, the DFG is required by the California Endangered Species Act to provide studies in support of lead agency projects

"to ensure that any action authorized, funded or carried out by that state lead agency is not likely to jeopardize the continued existence of any endangered or threatened species. ...the department [DFG] shall issue a written finding based on its determination of whether a proposed project would jeopardize the continued existence of any endangered or threatened species or result in the destruction or adverse modification of habitat essential to the continued existence of the species. ...The department shall base its determination on the best available scientific information."

"If jeopardy is found, the department shall determine and specify to the state lead agency reasonable and prudent alternatives consistent with conserving the species which would prevent jeopardy to the continued existence of the species or the destruction or adverse modification of the habitat essential to the continued existence of the species."

Almost all of the work of the Central Valley Bay-Delta Branch is under contract to support the above statutes, regulations and decisions. In support of these and related statutes and regulations the CVBDB presently has 32 study projects. Some projects are jointly carried out with other agencies. All projects have the common elements of data collection (sampling) recorded in the field on paper forms, key data entry, data analysis and report generation. In addition, some projects include laboratory analysis and its resulting data generation.