The mission of the Natural Resources Agency is to restore, protect and manage the state's natural, historical and cultural resources for current and future generations using creative approaches and solutions based on science, collaboration and respect for all involved communities. The Secretary for Natural Resources, a member of the Governor's Cabinet, sets the policies and coordinates the environmental preservation and restoration activities of 27 various departments, boards, commissions, and conservancies, and directly administers the Sea Grant Program, California Environmental Quality Act (CEQA), River Parkways, and the Sierra Nevada Cascade grant programs.

The Natural Resources Agency consists of the departments of Forestry and Fire Protection, Conservation, Fish and Game, Boating and Waterways, Parks and Recreation, and Water Resources; the State Lands Commission; the Colorado River Board; the San Francisco Bay Conservation and Development Commission; the State Reclamation Board; the Energy Resources Conservation and Development Commission; the Wildlife Conservation Board; the Delta Protection Commission; the California Conservation Corps; the California Coastal Commission; the State Coastal Conservancy; the California Tahoe Conservancy; the Santa Monica Mountains Conservancy; the Coachella Valley Mountains Conservancy; the San Joaquin River Conservancy; the San Gabriel and Lower Los Angeles Rivers and Mountains Conservancy; the Baldwin Hills Conservancy; the San Diego River Conservancy; the Sierra Nevada Conservancy; Sacramento-San Joaquin Delta Conservancy; Delta Stewardship Council; and the Special Resources Program.

Chapter 5, Statutes of 2009, Seventh Extraordinary Session establishes the Delta Stewardship Council and the Sacramento-San Joaquin Delta Conservancy in the Natural Resources Agency and shifts CALFED resources to these new entities. The Delta Stewardship Council is the successor to the CALFED Bay-Delta Program.