French Frigate Shoals is an atoll consisting of a large, crescent-shaped reef surrounding numerous small, sandy islets. While the land area is only square kilometer (67 acres), the total coral reef area of the shoals is over 938 square kilometers (232,000 acres).

French Frigate Shoals exhibits the classic features of a well-developed coral atoll. The coral growth is atop an eroded volcano, which has been submerged for millions of years. A steep-sided basalt pinnacle juts out of the water in the center of the atoll. This unique rock formation is the last remnant of the original volcano. The pinnacle was named "La Pérouse Pinnacle" after Compte de La Pérouse, who visited the atoll in 1786.

Tern Island, a part of the atoll, was formed into a runway to serve as a refueling stop for planes enroute to Midway during World War II. The original seawall, runway, and some of the buildings remain. The U.S. Fish and Wildlife Service continues to maintain a field station there, which is staffed year-round by two permanent employees and a handful of volunteers.

The reef system associated with French Frigate Shoals supports the greatest variety of coral species in the NWHI. These include table, finger, and lobe corals. It also supports more than 600 species of invertebrates such as sponges, coral worms, snails, lobsters, crabs, shrimps and clams, oysters, sea urchins, and sea stars. Many of these are endemic species.

More than 150 species of algae live among the reefs, including red, green and brown algae. The outer reef waters support gray reef sharks, butterfly fish, and large schools of jacks and groupers.

Hundreds of green sea turtles inhabit French Frigate Shoals. Over 90% of the threatened Hawaiian population of green sea turtles travel to the shoals for safe nesting. Satellite tagging of these turtles indicates that most of them migrate to the Main Hawaiian Islands to feed before returning to French Frigate Shoals to breed. Some of these turtles travel northwest to feed, while others travel as far south as Johnston Atoll.

The many small islets of French Frigate Shoals provide refuge to the largest population of endangered Hawaiian monk seals. Preserving this atoll is critical to their survival.