Santee Refuge encompasses an exceptional diversity of habitats including open water, closed hardwood canopies, cultivated fields, freshwater marshes, cypress swamps and upland pine areas. Significant waterfowl concentrations winter on the refuge including the largest group of Canada geese belonging to the Southern James Bay population in the state. The refuge hosts which is thought to be the furthest inland nesting area for Painted Buntings in South Carolina. Nesting Bald Eagles and Osprey are evident along with other birds of prey. Great Blue Heron and Anhinga rookeries are found on two refuge units. During spring and summer drawdowns, a variety of shorebirds are attracted including Greater Yellowlegs and 11 recorded sandpiper species. In addition, the refuge is occaisionally visited by five plover species with the Semipalmated Plover the most common visitor. Forty Wood Storks and a small flock of Sandhill Cranes utilize the refuge each year. Among the 296 species recorded on the refuge are a total of 16 species of sparrows including LeConte's, Vesper, Henslow's and Lincoln's. Managed and fallow fields on the Cuddo, Pine Island and Bluff units provide good habitat for these and other grassland bird species.
Santee National Wildlife Refuge is an important bird area primarily for its large numbers of wintering waterfowl. Located in the inland portion of the lower coastal plain, it is a large area of undisturbed land surrounded by a power reservoir with an increasing number of residential developments. Santee National Wildlife Refuge has a variety of habitats that attract shorebirds as well as migrating neotropical species. The area is managed actively for waterfowl although the shorebirds also benefit from this practice. Bald Eagles breed on the site and there large numbers of breeding Wood Ducks.
Invasion of non-native aquatic plants into impoundments, water pumping areas, and canals used to flood waterfowl areas, develpment of the surrounding area for recreational homes, increased hunting pressure offsite and the manipulation of the water level of Lake Marion.
Santee National Wildlife Refuge is administered by the U.S. Fish and Wildlife Service, an agency within the Department of Interior. Marc Epstein is the refuge manager.
Dominant plant communities include mixed loblolly pine/hardwood, bottomland hardwood (oak/maple/hickory), warm season grassland fields, cypress-tupelo, and moist soil plant communities. The topography is flat and the soils are predominantly clay loam and sandy loam.
The land use on the refuge is overwhelmingly natural conservation as befits a national wildlife refuge. The agricultural fields are planted to enhance the food supply for the wildlife, typically waterfowl. The is very limited hunting and the small amount of ecotourism is captured using self-guiding nature trails.