From: USFW, 1982; SRWMD, 2002; Florida DEP, 2003
The Suwannee River Basin contains almost 29,500 square km beginning in the Coastal Plain of Georgia near Cordele and flowing through much of north Florida before emptying into the eastern Gulf of Mexico. The Suwannee River is part of the Florida State park system and the Withlacoochee River joins it within this park. The Aucilla, Econfina, Fenholloway, Steinhatchee, Suwannee, Waccasassa and Withlacoochee Rivers all drain into the estuarine areas of the Florida coast, with the Suwannee River providing 60% of the total freshwater discharge (298.5 cubic m/sec annually).

Surface waters in the region are all affected by groundwater inflow from an extensive regional aquifer characterized by limestone, or karst, topography. It is one of the most undeveloped, unpolluted regions in Florida. The area is dominated by coastal marshes which includes (N to S) Deadman Bay, Horseshoe Cove, Suwannee Sound, the Cedar Keys, Waccasassa Bay and Withlacoochee Bay. The Cedar Key area represents the northernmost limit of distribution of mangroves on the Florida Gulf coast. The region supports the second largest seagrass area in the eastern Gulf of Mexico (3,000 sq. km), with oyster bars also representing dominant submerged habitats. Landward of the coastal marshes, forested hydric hammock wetland communities are characterized by periods of short but possibly deep inundation, and may be flooded several times during the course of the year.