Two islands (East Marin and West Marin) form the core of Marin Islands National Wildlife Refuge. The 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, which had housed two vacation homes, 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. The refuge was established in 1992 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.