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.

Eighty-three reefs, rocks and islands in the San Juan Islands of northern Puget Sound have been set aside as San Juan Islands National Wildlife Refuge. These islands have also been designated by Congress as a wilderness area where seabirds, eagles, and marine mammals will have an undisturbed place to live and raise their young.

Several islands have high cliffs and grassy slopes where seabirds such as cormorants, pigeon guillemots, and gulls prefer to nest. Bald eagles, a threatened species, build their nests high in the large trees of forested islands and catch fish in the surrounding waters. Harbor seals haul out to rest or to have their pups on the smaller rocks and reef, as well as on the rocky beaches of the larger islands.

Of the 700 or so islandsislets, rocks, and reefs that make up the San Juan Islands, 83 are part of the refuge. Of these, 81 have been designated Wilderness since 1976.