Natural features in the park include old-growth cypress swamps, old-growth floodplain forests, upland hardwood forests and an longleaf pine forest. Located within the hardwood forest are three state champion trees, the Sassafras, American Beech and American Basswood.

There is an abundance of wildlife at Wakulla Springs due to the pristine river and sanctuary. Among the wildlife in the park are native birds, such as limpkin, purple gallinules, heron, egret, bald eagle, anhinga, osprey, black and turkey vultures, and white ibis. In the winter, water fowl present in the park include American widgeon, hooded merganser, American coot, wood ducks, and greater and lesser scaup. Alligators, snakes, and turtles are often seen on the river bank or sunning on logs in the water. Due to the various plant communities present, white-tailed deer and wild turkey can also be seen in the park.