Trees, shrubs and vines vary with elevation and soils. Cabbage palm is more abundant on higher elevations. Huge stumps are reminders of impressive bald cypress that once dominated the overstory before logging. Cypress regeneration has been uneven. Red maple, sweet gum, winged elm, magnolia, ashes, and red cedar now dominate the overstory in some portions of the swamp. The understory varies with elevation as well; palmetto, American beautyberry, grape vines, ferns, swamp dogwood, dahoon holly and wax myrtle are common. The swamp stores and cleanses water entering the Chassahowitzka estuary. For a diverse range of wildlife, the swamp means food, shelter and denning and nesting sites.
Scattered throughout the uplands, cypress domes consist of pond cypress, bald cypress, red maple, sweet gum, willow and buttonbush. Historically more cypress domes existed in the area. Logging operations removed most of the cypress from the ponds before converting the landscape to pine plantations.
Freshwater marshes are found in low areas with high water tables in the sandhills and flatwoods as well as along inland creeks. Sawgrass is the most common freshwater marsh plant. Freshwater marshes support numerous wading birds, fish and alligators.
Scattered throughout the sandhills, wet prairies are dominated by herbaceous species that produce a colorful flush of wildflowers in the fall. White tops, spike rushes, bog buttons, dahoon holly, American lotus, spatter dock and grasses are common.
Tidal marsh extends from the Gulf to tidal creeks. Common plants are black needle rush and smooth cordgrass. As creeks change from brackish to fresh, sawgrass becomes common. Red cedar, cabbage palms, and live oaks occur on islands of high ground and along the creeks. Although salt marshes appear visually uniform, they are among the most biologically rich communities on earth. Salt marshes are protected spawning and nursery areas for thousands of marine organisms and feeding grounds for a host of terrestrial and aquatic animals. They also produce abundant nutrients carried by the tide to the sea.
Longleaf pine or slash pine flatwoods have a saw palmetto, wax myrtle and gallberry understory. This habitat is generally found on relatively flat, moderate to poor soils, sometimes with low surface water availability. Flatwoods have also been degraded by lack of fire. In some places, the wax myrtle/gallberry understory exceeds eight feet and is so dense that quality wildlife forage has been eliminated.
Wiregrass, palmettos and forbs grow beneath a canopy of scattered longleaf or sand pine, blackjack oak and turkey oak, is found wiregrass, palmettos and forbs. Because of timbering, large pines are scarce. Species richness is also low in most areas because of fire suppression prior to state purchase. A keystone species of the sandhill community is the gopher tortoise. Nearly 350 species of animals, including the threatened Eastern indigo snake and the rare Florida mouse use gopher tortoise burrows. Several species of insects are found only in gopher tortoise burrows.
Remnants of scrub grow on a ridge of historic dunes running parallel to the coast about 3 to 4 miles inland. Some of the rarest plants and animals in the world are found in Florida scrub communities. In the past, the scrub in Chassahowitzka was protected from fire and as a result was in poor condition when the area was purchased by the state. Common species include sand pine, myrtle oak, and scrub live oak. When restored, scrub on the Weeki Wachee tract may become home once again to the threatened Florida scrub-jay.