Mesic flatwoods are the most extensive plant community on Little Gator Creek WEA. The habitat occurs on relatively flat, poorly drained terrain. The pine canopy consists of slash and longleaf pines. Saw palmetto is the most common shrub, although dwarf live oak, staggerbush and dwarf blueberry are also common. Wiregrass is the dominant species in the varied ground cover. Because of pine harvests early in the 20th century, most of the pines are younger than 75 years old. This high quality habitat has been maintained by regular prescribed burning. The imperiled fall-flowering celestial lily occurs here and is well-adapted to regular fire.
Two basin swamps on Little Gator Creek occupy depressions that were probably once oxbows or swales within the Withlacoochee River floodplain. The canopy and subcanopy are dominated by pond cypress, red maple and swamp laurel oak. The canopy trees in the basin swamp are approximately 50 years old. The shrub layer is fairly open, with scattered cabbage palm, wax myrtle, shiny fetterbush and blueberry. Herbs are generally sparse in basin swamps due to high water and low light. Maidencane and Virginia chain fern are the most common herbaceous species.
Little Gator Creek is located in the confluence of Gator Creek and the Withlacoochee River, and hydric hammocks are found in the floodplains of both. The canopy and subcanopy of these forests are dominated by laurel oak, live oak and water oak, with red maple, tupelo gum and cabbage palm also common. Common shrubs include cabbage palm and yaupon holly. The hydric hammock on the WEA contains two small patches of pond cypress-dominated floodplain swamp in a low area closer to the Withlacoochee River. The vegetation resembles hydric hammock except bald cypress is a canopy dominant.
Nine dome swamps of varying sizes occur on Little Gator Creek WEA. Most are dominated by pond cypress with a large hardwood component of red maple, sweet gum and swamp laurel oak. Wax myrtle and persimmon occur in the understory. The sparse herbaceous layer has saw grass, maidencane, sedges and duckweed.