The Florida Reef is the only living coral barrier reef in the continental United States. It is the third largest coral barrier reef system in the world (after the Great Barrier Reef and Belize Barrier Reef). It lies a few miles seaward of the Florida Keys, is about 4 miles (6 to 7 km) wide and extends (along the 20 meter depth contour) 270 km (170 mi) from Fowey Rocks just east of Soldier Key to just south of the Marquesas Keys. The barrier reef tract forms a great arc, concentric with the Florida Keys, with the northern end, in Biscayne National Park, oriented north-south and the western end, south of the Marquesas Keys, oriented east-west. The rest of the reef outside Biscayne National Park lies within John Pennekamp Coral Reef State Park and the Florida Keys National Marine Sanctuary. Isolated coral patch reefs occur northward from Biscayne National Park as far as Stuart, in Martin County. Coral reefs are also found in Dry Tortugas National Park west of the Marquesas Keys. There are more than 6,000 individual reefs in the system. The reefs are 5,000 to 7,000 years old, having developed since sea levels rose following the Wisconsinan glaciation.

The densest and most spectacular reefs are found to the seaward of Key Largo (in and beyond John Pennekamp Coral Reef State Park) and Elliott Key where the two long keys help protect the reefs from the effects of water exchange with Florida Bay, Biscayne Bay, Card Sound and Barnes Sound. The bays and sounds (all between the Florida Keys and the mainland) tend to have lower salinity, higher turbidity and wider temperature variations than the water in the open ocean. Channels between the Keys allow water from the bays to flow onto the reefs (especially in the middle Keys), limiting their growth.