Crocodile Lake National Wildlife Refuge was established in 1980 to protect critical breeding and nesting habitat for the endangered American crocodile and other wildlife. The refuge is located in north Key Largo and is currently comprised of 6,700 acres including 650 acres of open water. It contains a mosaic of habitat types including tropical hardwood hammock, mangrove forest, and salt marsh. These habitats are critical for hundreds of plants and animals including six federally-listed species.

Crocodile Lake NWR is unusual in that not all of the critical habitat areas are in a pristine, undisturbed condition. A large portion of the refuge was going to be a residential development complete with canals for boating access. The dredge-spoil from the canal system was piled up in berms on the banks of the canals and became an important nesting area for the federally-listed American crocodile. American crocodiles are fairly wide-spread throughout the tropics, however, in the U.S. crocodiles are only found in south Florida and the Keys.

The refuge protects one of the largest remaining tracts of tropical hardwood hammock which is a globally threatened habitat type. These diverse forests are home to hundreds of plants and animals including the federally-listed Key Largo woodrat, Key Largo cotton mouse, Schaus swallowtail butterfly, Stock Island tree snail, and Eastern indigo snake. These species require hammocks in order to survive. Unfortunately, most of the hammocks in Key Largo have been eliminated by development which has lead to considerable population declines in these already imperiled species.