San Juan Islands Refuge consists of 83 rocks, reefs, grassy islands, and forested islands scattered throughout the San Juan Islands of northern Puget Sound. These islands, totaling almost 450 acres, were set aside to protect colonies of nesting seabirds, including pigeon guillemots, double-crested cormorants, and pelagic cormorants.

They also attract a variety of other wildlife, including bald eagles and harbor seals. In order to help maintain the natural character of these islands, all the refuge islands except Matia and Turn are closed to the public.