The19,000-acre refuge consists of the Gautier, Ocean Springs, Fontainebleau, and Bluff Creek units. Wet pine savannas, pine scrub, forested swamps, and tidal marshes are the main habitat types of the refuge.
The original presettlement vegetation consisted mostly of pine savannas. Ecological characteristics contributing to these communities include high rainfall, low flat topography, clay soil with a hard subsurface pan leading to an infertile, acidic, waterlogged soil. The high natural fire frequency kept the areas open, with grasses like wiregrass providing much of the fuel. Fire suppression allowed pines and shrubs to invade and out compete the native savanna plants. In the 1960s and 1970s, much of the remaining open savanna was converted to pine plantation by planting and ditching, the latter disrupted the natural water regime. Less than five percent of the original acreage of this habitat remains in the Atlantic/Gulf Coastal Plain making it one of the most endangered ecosystems in the country. The refuge savannas are considered the last remaining large patches.
The savannas are large wet prairies with numerous species of low-growing grasses, sedges, and herbaceous wildflowers, with occasional longleaf pines, pond cypresses, or low-growing shrubs. The tree cover only ranges between one and five percent. The plant species diversity is large, one of the highest in North America, particularly those of the ground cover species. Of special interest are the orchids and many carnivorous plants. The wetter areas are also refered to by other names such as pitcher plant bogs.
The typical grasses and sedges of the savanna are Andropogon, Aristida, Ctenium, Muhlenbergia, Rhynchospora and Scleria. Common herbs include Aletris, Asclepias, Aster, Balduina, Bigelowia, Calopogon, Drosera, Eriocaulon, Eupatorium, Hypoxis, Lachnanthes,Lophiola, Pogonia, Polygala, Rhexia, Sarracenia, Tofieldia, Utricularia, Xyris and Zigadenus. The usual low-growing shrubs of the savanna are Gaylusaccia, Hypericum, and Vaccinium.
Forested swamps are forested wetlands found in low drains through the pine savannas and include cypress-tupelo drains and forested bayheads. These would include Perigal Swamp, Turcotte Drain, Ben Williams Swamp, and numerous other drains. They are characterized by trees in the mid-story and over-story with a shrub layer and sparse herbaceous ground layer. Common trees include cypress (Taxodium), slash pine (Pinus elliottii), bays (Magnolia, Persea), buckwheat (Cliftonia racemiflora, Cliftonia monophylla), red maple (Acer rubrum), swamp tupelo (Nyssa biflora) , sweetgum (Liquidambar styraciflua), and swamp oaks (Quercus). Shrubs include gallberry and other hollies (Ilex spp.) and wax myrtle (Myrica). Peat moss (Sphagnum) is sometimes found in large mats. Ferns, sedges, and rushes are common in the herbaceous layer. Swamps burn infrequently because of the high humidity, standing water, moist fuel, and shelter from wind.
Pine scrub is a "mixed-bag" classification that includes natural pine flatwoods and former pine savannas now overgrown with slash pine. It also includes numerous shrubs including Ilex and others because of the effects of long-term fire suppression and pine plantations. Very few of the native wildlflowers and sedges remain, having been choked out by these woody plants that were formerly kept at bay by frequent surface fires.
Tidal marshes are the bayous of Bluff Creek and Bayou Castelle, replacing the forested swamps in the intertidal zone. They are covered by vast areas of sawgrass (Cladium jamaicense) with herbaceous species intermixed along the edges. All these species are adapted to the saturated soils caused by incoming tides. In part of the Fontainebleau unit, closer to the coast where the salinity gets higher, sawgrass is replaced with saltmeadow cordgrass (Spartina patens) and needlegrass rush (Juncus roemerianus). .