Alligators are native only to the United States and China. The majority of American alligators inhabit Florida and Louisiana, with over a million alligators in each state. Southern Florida is the only place where both alligators and crocodiles live side by side. American alligators live in freshwater environments, such as ponds, marshes, wetlands, rivers, lakes, and swamps.

Although most U.S. national parks preserve unique geographic features, Everglades National Park was the first created to protect a fragile ecosystem. The Everglades are a network of wetlands and forests fed by a river flowing .25 miles per day out of Lake Okeechobee, southwest into Florida Bay. The Park is the most significant breeding ground for tropical wading birds in North America, contains the largest mangrove ecosystem in the western hemisphere, is home to 36 threatened or protected species, and supports 350 species of birds, 300 species of fresh and saltwater fish, 40 species of mammals, and 50 species of reptiles. The majority of South Florida's fresh water, which is stored in the Biscayne Aquifer, is recharged in the park.

The Silver River flows through an undeveloped woodland just to the west of the Ocala National Forest; the water quality is considered excellent, and the river is regarded as being in pristine condition. Many types of turtles are found in the Silver River, while ospreys and anhingas breed along its banks. The Silver River is designated under the Outstanding Florida Waters program.

Three Sisters Springs are located on the Crystal River, in Florida. They are in a natural inlet on the east side of Kings Bay. They contain three spring areas that contain many sand boils and vents. The land surrounding the springs is privately owned property and there is no landfall or boat tie up permitted. Only kayaks, canoes, and swimmers are permitted in the area. Three Sisters Springs is also home to many of the local manatees and is one of the Crystal Rivers group of sanctuaries.

Pelican Island National Wildlife Refuge is a United State National Wildlife Refuge located just off the western coast of Orchid Island inIndian River Lagoon east of Sebastian, Florida. The refuge consists of a 3-acre (12,000 m2) island that includes an additional 2.5 acres (10,000 m2) of surrounding water. Established by President Roosevelt in 1903, Pelican Island was the first national wildlife refuge in the United States. It was created to protect egrets and other birds from extinction through plume hunting.