Peak nesting totals for green sea turtles have increased over 600% from 1990 to 2007, but have grown almost exponentially in the past handful of years. Peak nesting totals for leatherbacks have increased over 900% since 1990. Greens and leatherbacks reached all-time highs in 2016 and 2014 respectivly, with over 14,152 green turtle nests and 79 leatherback nests. After 1990, loggerhead nesting totals increased until 1998, and then decreased until reaching an all-time low in 2007 with 7,905 nests. Loggerhead nesting totals have begun to increase again since 2007.

The Archie Carr NWR rivals the beaches of Masirah Island at the Sultanate of Oman as the most important loggerhead nesting beach in the world. About 90% of the world’s loggerhead population nests in Florida and Oman. Due to decreased nesting in Oman the Carr Refuge has become the most important nesting beach for Loggerheads. Further, the refuge provides connectivity to the Indian River Lagoon and Pelican Island NWR, which provide very important foraging habitat for juvenile sea turtles.

Five sea turtle species are found in Florida's marine and estuarine waters: green, hawksbill, Kemp's ridley, leatherback, and loggerhead. Sea turtles have declined world-wide due to factors such as human consumption, entrapment in fishing gear, and loss of nesting habitat. In addition, beach front lights can discourage females from nesting and can disorient hatchlings. These aquatic reptiles rarely come on shore, usually only to lay their eggs on the beach, well above the high tide mark. Three species are known to regularly nest on the refuge: green, leatherback, and loggerhead. Hawksbills have been documented on the refuge, but very rarely. Kemp's ridley sea turtles, the rarest species, have had documented nesting on the refuge since 2013.