Michigan Islands National Wildlife Refuge is comprised of eight islands in Lakes Michigan and Huron. Thunder Bay and Scarecrow islands in Thunder Bay (near Alpena, MI), and Big and Little Charity islands in Saginaw Bay are managed by Shiawassee National Wildlife Refuge in Saginaw, MI. Seney National Wildlife Refuge has management resonsibility for Gull, Pismire, Hat, and Shoe islands, part of the Beaver Island Group in the northern portion of Lake Michigan. In 1970, Scarecrow, Pismire, and Shoe islands were officially designated as Michigan Islands Wilderness Area. Big Charity and Thunder Bay islands have lighthouses and keeper's quarters.

Michigan Islands National Wildlife Refuge (NWR) is not staffed and is closed to public entry. The four islands in Lake Michigan are part of the Beaver Island Archipelago in the northern portion of the lake and are managed by the Seney NWR.

Five of the islands in the refuge are located in Lake Huron and can be found in Saginaw Bay and Thunder Bay. These islands are managed by the Shiawassee NWR.