The park has a wide variety of birdlife because of the many varying habitats from uplands to wetlands including the vast dunes, lakes, streams, hardwood forests, and cedar swamps. Bald eagles are seen along the Lake Michigan shoreline. The sound of loons can be heard on the lakes. The sandy beaches are home to shorebirds including increasing numbers of the endangered piping plover. The forests are habitat for many warblers, thrushes, broad-wing hawks, red-tailed hawks, and great-horned and barred owls. Warblers and hawks are easily seen in the spring as they migrate along the coast and rest on the islands in their flight across Lake Michigan. Upland sandpipers, bobolinks, and grasshopper sparrows are some of the birds that are in decline nationally but are readily found in park meadows. The many lakes and streams in the park exhibit waterfowl such as wood duck, blue-winged teal, hooded mergansers and buffleheads. Old field succession stages are sites for woodcock nesting. Sandhill cranes can be found in some wet meadows. In the winter there are great rafts of goldeneyes, mergansers and scaup on Lake Michigan.
Habitats of special interests include the miles of fore-dunes along Lake Michigan with vegetation of brushy scrubs of juniper, grasses and small pines. This is the nesting habitat of the prairie warbler, which is one of Michigan’s threatened species. There are segments of mature hardwood forests in the park. Some of the least disturbed of these forests are on South Manitou Island where ovenbirds and veeries are common. The park is concerned about fragmentation of these forests and the potential for loss of nests of neo-tropical birds due to predation and parasitism. Many of the old roads on South Manitou and North Manitou Islands have filled in with natural vegetation which benefits these bird species.