Birds are the most easily observed animals in the park. Spring and Fall migration brings a number of different species through the park. Stormy weather can drive a few pelagic birds in from the open ocean for a visit. In summer, a number of tern species, egrets, black skimmers, herons, piping plovers and other shorebirds nest within the park's boundaries.
Mammals are uncommon on the islands; rice rats, rabbits, river otters, and raccoons are some of the native species found here. On Shackleford Banks is a population of horses that has gone wild and adapted to their environment over the past few hundred years.
Although salt and brackish water environments dominate the islands, a few fresh water habitats support tree frogs and Fowler's toads. While diamond-back terrapins prefer the salt marsh areas, the grasslands are the preferred habitat for five-lined racerunner lizards and black racer snakes.