The California Bay-Delta Authority coordinated 24 state and federal agencies to implement a long-term comprehensive plan to restore ecological health and improve water supply reliability in the San Francisco Bay/Sacramento-San Joaquin Delta system.

Effective July 1, 2006, Chapter 77, Statutes of 2006 reorganized the CALFED Bay-Delta Program and transferred the functions of the California Bay Delta Authority to other departments and agencies. The executive management and Science Program functions were transferred to the Secretary for Resources (organization code 0540), the Ecosystem Restoration Program functions to the Department of Fish and Game (organization code 3600), the CALFED Bay-Delta administrative functions to the Department of Forestry and Fire Protection (organization code 3540), the Water Quality program functions to the State Water Resources Control Board (organization code 3940), and the Levees and Water Use Efficiency program functions to the Department of Water Resources (organization code 3860).