The remainder of the beaches, including those at the Marquesas Keys, are open during daylight hours for compatible, wildlife-oriented recreational uses such as wildlife observation, nature photography, and environmental education.

The Refuge includes mostly mangrove islands, with a few sandy beaches and dunes that are critical nesting habitat for endangered sea turtles.

Other habitat includes salt marsh and coastal berm hammocks, plus sea grass and coral reef communities.

The area managed is overwhelmingly (99 percent) marine environment including large sand flats surrounding the islands that are used extensively by wading birds when they forage.

The refuge protects habitat for a wide variety of birds, including nesting or wintering populations of terns, magnificent frigatebirds, white-crowned pigeons, ospreys, and great white herons.