Peregrine falcons and bald eagles use refuge lands during spring and fall migration. Eagles also nest on remote, forested islands and over-winter here where they can feed on fish and carrion. Roseate terns nest with other terns on some of the grass-covered islands. Marine mammals also use this region extensively. Harbor seals are here throughout the year, using refuge and other islands for loafing, basking and giving birth to their pups.
Gray seals are less common but are present year-round, usually on the outer islands.
Harbor porpoises, finback and minke whales, and endangered right whales occasionally explore the bays seeking the rich supply of fish and invertebrates providing by ocean upwellings near islands and ledges. On Petit Manan Point and some of the larger islands deer, bobcats, foxes, coyotes, porcupines, snowshoe hares, beaver and raccoons are common. Moose and black bear are also sometimes seen. Managing for Wildlife Habitat protection is the most important management goal for these refuges, but refuge staff also actively manage certain areas and populations for key species in need of help. Biologists monitor population trends and nesting success for many species.