The Pinckney Island NWR bird list contains over 250 species. The most popular and colorful is the painted bunting, a common summer resident on the island and in the area’s brushy habitat. In fall and early winter, warblers are common in the live oaks and scrub/shrub habitat. Waterfowl, shorebirds, wading birds, raptors, and neotropical migratory birds are common on the refuge. The refuge is one of the best places in South Carolina to see breeding, yellow-crowned night herons. Other wading bird breeders include: snowy egrets, cattle egrets, tri-colored herons, little blue herons, and black-crowned night herons. These herons are joined in the summer by a few non-breeding wood storks.
A variety of reptiles, amphibians, fish, and mammals inhabit the refuge and the waters nearby. Some of the more common snake species include the cottonmouth, black racer, corn snake, and yellow and grey rat snake. Mammals common to the refuge include white-tailed deer, bobcats, raccoons, opossums, eastern gray squirrels, fox squirrels, river otters, and red foxes.