In 1909, President Theodore Roosevelt established the Farallon National Wildlife Refuge as a preserve and breeding ground for marine birds. The Refuge originally encompassed only the North and Middle Farallon Islands and Noonday Rock. In 1969 the Refuge was expanded to include the South Farallon Islands. The Farallon Islands National Wildlife Refuge, as it was renamed in 2017, is one of 562 National Wildlife Refuges managed by the U.S. Fish and Wildlife Service across the U.S.

The islands are surrounded by a marine area that is designated a California State Marine Reserve (established in 2010) managed by the California Department of Fish and Wildlife and within the Greater Farallones National Marine Sanctuary (established in 1981) managed by the National Oceanic and Atmospheric Administration.