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 26 various departments, boards, commissions, and conservancies, and directly administers the Sea Grant Program, California Environmental Quality Act, and River Parkways.

The Natural Resources Agency consists of the departments of Forestry and Fire Protection, Conservation, Fish and Wildlife, Parks and Recreation, and Water Resources; the State Lands Commission; the Colorado River Board; the San Francisco Bay Conservation and Development Commission; 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; the Sacramento-San Joaquin Delta Conservancy; the Native American Heritage Commission; the California Science Center, and the Special Resources Program.

The 2013-14 Governor's Budget proposes to consolidate oversight of ocean protection functions within the office of the Secretary of the Natural Resources Agency to improve the efficiency and coordination of this effort. Therefore, the Ocean Protection Council, which was formerly administered by the State Coastal Conservancy, is now included here. The mission of the California Ocean Protection Council is to ensure that California maintains healthy, resilient, and productive ocean and coastal ecosystems for the benefit of current and future generations. The Budget also reflects the transfer of the California Science Center from the State and Consumer Services Agency to the Natural Resources Agency in 2013-14, as the Science Center's mission more closely aligns with that of this agency.