Island environments, naturally isolated, provide important habitat for numerous bird species, mammals, plants, amphibians and aquatic species. Wildlife species are characteristic of the southern limits of the boreal and northern limits of the hardwood/hemlock forests. Game species include whitetail deer, black bear, snowshoe hare, waterfowl, woodcock, and ruffed grouse. Other fur-bearers include the red fox, coyote, beaver and otter. Small mammals are an important component of the lakeshore's terrestrial fauna and include: shrews, mice, voles, red squirrels and chipmunks. Some common mainland species do not occur on the islands, including raccoon, skunk, porcupine, gray squirrel, chipmunk and woodchucks.
The Apostle Islands area is important for commercial and recreational fishing. Shoals near the lakeshore's ¼ mile lakeward boundary provided critical spawning areas for the commercially important lake trout and whitefish. The fish community presently found within the relatively shallow Apostle Islands waters is diverse and complex for waters such as Lake Superior.
The islands within the park provide important habitat for resident breeding birds as well as neotropical migrants. The great majority of nesting forest bird species in the Apostle Islands are migratory. The lakeshore includes important migratory bird concentration points during spring and fall migration.