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.

The islands provide habitat for migratory birds and colonial nesting birds. They are also home to the Federally threatened dwarf lake iris and Pitcher's thistle. Island habitats vary considerably, including cobblestone beaches, grasses and wildflowers above the high water line, shrub-covered sand dune areas, interior mixed hardwoods, balsam fir, and white cedar. Big Charity Island also has an 11-acre inland lake. Soils consist of shallow organics or sands over cherty limestone and dolomite. The islands are used for nesting by American redstarts, herring and ring-billed gulls, double-crested cormorants, great blue herons, black-crowned night herons, and common and Caspian terns.

Thunder Bay Island is a rare, distinctive, alvar ecological community with a little bluestem alvar grassland, alvar pavement, and a limestone bedrock lakeshore.

Big Charity and Thunder Bay islands have lighthouses and keeper's quarters.