Marin Islands National Wildlife Refuge was established in 1992, and is managed as part of the San Francisco Bay National Wildlife Refuge Complex. It is located in San Pablo Bay off the coast of San Rafael in Marin County, California. Two islands (East Marin and West Marin) form the core of the refuge; surrounding submerged tidelands also are part of the refuge.

West Marin Island, rises 85 feet above the bay's waters and supports the largest heron and egret rookery in the San Francisco Bay area. Nesting species include great egrets, snowy egrets, great blue herons, and black-crowned night herons. East Marin Island, a former vacation retreat, now supports a variety of introduced and native plants and provides critical nesting material and rest sites for the nearby colony.

Submerged tidelands support a variety of resident and migratory water birds such as surf scoter, black oystercatcher, diving ducks, and osprey. Refuge objectives are to protect migratory species, including the heron and egret nesting colony, protect and restore suitable habitat for the colony, and protect the tidal mud flats and unique island ecosystem.