In addition to its extensive list of birds, Blackwater harbors a variety of mammals, including bats, raccoons, rabbits, otters, opossums, skunks, and the elusive red fox. Muskrats are common in the marsh, as is the larger nutria, a South American rodent introduced to this country in the 1930's. The nutria population on the Refuge has greatly increased causing considerable wetland damage. White-tailed deer can sometimes be seen in wooded areas and in fields along the forest edge. Sika deer, a species native to Asia, that were introduced to nearby James Island in 1916, prefer the wet woodlands and marsh.
Sika deer are more nocturnal than white-tailed deer and, therefore, are less likely to be seen.
Both gray squirrels and the endangered Delmarva fox squirrels inhabit the wooded areas. Waterfowl Refuge programs specifically designed for waterfowl include management of the brackish marsh to produce succulent natural foods and management of impoundments to provide freshwater habitat. A variety of crops are planted and native plants encouraged, providing a array of foods to meet the nutritional needs of migrating and wintering waterfowl. Although waterfowl hunting is not permitted on the Refuge, hunting is allowed on surrounding private lands and state wildlife management areas. Furbearers A winter trapping program, regulated by the Refuge and accomplished by trappers under special permit, provides protection for fragile marsh vegetation by reducing the impact of foraging furbearers like the nutria.