In addition to being one of only three breeding populations of the American crocodile,[2] the refuge is home to tropical hardwood hammock, mangrove forest, and salt marsh.

Crocodile Lake National Wildlife Refuge was once entirely platted for residential development; however, accumulated deposits of dredge-spoils on the bayside of North Key Largo became an important nesting area for some of the country's remaining American crocodiles[1] which have recovered in recent years from a low, in 1975, of approximately 200 in population size.

Due to the once almost unrestricted commercial and residential development of the Florida Keys, the size and number of fragmented tropical hardwood hammock habitat have been reduced.

These trees provide a critical home for this endangered animal; however, the woodrats are finding it harder to live because of the decreasing size of their hammock[1] habitat, and because of subsidized predation by free-roaming house cats.

During the day, Key Largo woodrats shelter in crevices and fissures in the island's limestone substrate, and under dense tangles of tree roots.

Crocodile Lake National Wildlife Refuge (CLWR) and Dagny Johnson Key Largo Hammock Botanical State Park (KLH) are separated by the County Road 905 right-of-way for approximately 10 miles (16 km).

Graduate student / biologist Joanne Potts and her assistant, Wildlife Refuge volunteer Clay DeGayner, were working in KLH and tracking a telemetry signal transmitted by one of several radio collars they had placed on a small number of woodrats.

The python also turned out to be the first vouchered (verified by a specimen or photograph) occurrence of its species found wild in the Florida Keys.

“There's a good chance we never would have found him,” said Scott Hardin, exotic-species coordinator for the state Fish and Wildlife Conservation Commission.

Here it's happened, and it has the potential to be a serious problem.”[6] Hardin later assumed the 7.5 feet (2.3 m) snake was either an escaped or released pet by someone who realized the python "[had] become a burden".

Recent remote camera work has identified cats throughout the refuge and KLH, with some perched on top of nest structures.

The base, constructed in an area which habituated the hammock, built numerous buildings and launch-pads to aid in war efforts.

[8] By the year 2000, the refuge had started plans for a project to remove unnecessary buildings and asphalt pavement from areas that had once been hardwood hammock.

[3] There is a 2.16 acres (8,700 m2) hole (officially known as the "Keystone Pit") in the refuge, which manager Steven Klett has wanted to fill in order to revitalize the hammock habitat.

The pit was dug 30 to 40 years ago in order to obtain fossilized coral to build and decorate fireplaces and other types of architecture (much of the limestone rock was mined as well).

According to an article published by McClatchy-Tribune Business News, "ever-growing piles of muck from widening U.S. 1 north of Key Largo could be used to fill in a gaping hole in the Crocodile Lake National Wildlife Refuge".