Habitats at the refuge include bay, brackish pond, impoundment, kettle holes, tidal flats, saltmarsh, freshwater marsh, upland shrub, grasslands, maritime oak forest, red cedar stands, and pioneer hardwoods. The strand habitats attract many beach using species including nesting piping plovers, roseate terns, least terns, common terns, harbor seals, and numerous shorebird species. The waters surrounding the refuge are considered critical habitat for juvenile Kemp's Ridley seaturtles and are also used by loggerhead sea turtles. Waterfowl use of the refuge is most heavy during the colder months, the most common being oldsquaw, white winged scoter, goldeneye and black ducks. The north/south axis of the peninsula also makes it serve as important habitat for migratory birds including shorebirds, raptors and songbirds.

During November, up to 100 each of common loons and horned grebes can be viewed from the refuge's beach. Morton provides habitat to several State and Federal endangered and threatened species, including piping plover, roseate tern, common tern, least tern, osprey, peregrine falcon, northern harrier, Kemp's ridley sea turtle and loggerhead sea turtle.

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