The Cape Fear Audubon Society, an organization that focuses on the conservation of bird species near Cape Fear, has 14 designated "Important Bird Areas." Among these are Battery Island and Green Swamp. Yellow-rumped warblers, American robins, red-headed woodpeckers and American crows are some of the region's arboreal birds, or species that spend most of their time in trees. Some of Cape Fear's wetland birds, or birds that live in freshwater habitats, are the great egret, great blue heron, white ibis and royal tern.
Cape Fear's location on the Atlantic Coast makes it home to marine mammal species. These mammals navigate through the region's saltwater estuaries near North Carolina's coastline. One marine mammal, the West Indian manatee, is native to the Cape Fear region. Due to overhunting and water degradation, West Indian manatees are on the endangered list. Federally and state protected areas, such as the Masonboro Island Coastal Estuarine Reserve and Holly Shelter Game Land, are home to mammals such as opossums, cotton rats, marsh rabbits, raccoons and river otters.
Various snakes make their home in North Carolina's Cape Fear region. Nonvenomous snakes use constriction to subdue their prey, while venomous snakes have fangs in their mouths to inject venom into their prey. Cape Fear's venomous snakes include the copperhead, eastern coral snake, eastern diamondback rattlesnake, cottonmouth, timber rattlesnake and pigmy rattlesnake. The rat snake, rainbow snake, eastern and southern hognose snakes, water snakes and scarlet snake are nonvenomous Cape Fear species. The Cape Fear region is also home to other reptile species such as turtles, alligators and skinks.
Cape Fear has lakes, rivers and ponds for freshwater fish, while saltwater fish live throughout the region's coastline and estuaries. Some of Cape Fear's estuary saltwater fish species are butterfish, black sea bass, bluefish and black drum. Other marine fish in the Cape Fear region live off the Atlantic coastline such as the bank sea bass, marlin, barracuda, tuna, mackerel and amberjack. Cape Fear's freshwater fish species include largemouth bass, speckled trout, walleye and the Cape Fear shiner, which is endemic to the Cape Fear River.