The South Florida Ecosystem Program is a collaborative effort by Federal agencies, working with State and local agencies, to help resolve land-use demands and water-supply issues in south Florida. The role of the U.S. Geological Survey in the program is to provide scientific insight into south Florida's hydrology and geology, which are an integral part of the fragile ecosystems of the Everglades, Florida Bay, and the Florida Keys. Historical changes in water-management practices to accommodate a large and rapidly growing urban population along the Atlantic coast, as well as intensive agricultural activities, have resulted in a highly managed hydrologic system with canals, levees, and pumping stations. These structures have altered the hydrology of the Everglades ecosystem, including Florida Bay. Currently, there are plans to change the quantity of water delivered to Everglades National Park and Florida Bay to restore the natural flow of the system.

Florida Bay, home to several endangered species, is a valuable breeding ground for marine life and an important recreational and sport fishing area. Florida Bay encompasses about 850 square miles in total area with an average depth of less than 3.5 feet. It is bordered by the mainland portion of Everglades National Park to the north, the Florida Keys to the east and south, and is open to the Gulf of Mexico to the west. During the last decade, Florida Bay has experienced algal blooms and seagrass die-offs which are signals of ecological deterioration that has been attributed to an increase in salinity and nutrient content of bay waters. Salinity and nutrient content are directly related to the amount and quality of freshwater that enters the bay and to flow patterns within the bay. Restoration of the Florida Bay ecosystem requires a better understanding of the linkage between the amount of water and nutrients flowing into the bay and the salinity and quality of the bay environment.