The Pleistocene ice pulses sculpted the islands and provided an abundance of till, and some glacial outwash, that covers most of the islands. Terraces, wave-cut benches, and elevated beaches show evidence of higher levels of Lake Superior. High bluffs of glacial material erode to provide sand for coastal seascapes of sandspits, beaches, tombolos and cuspate forelands (almost a spit but too stubby). The Apostles were glaciated repeatedly, most recently by the Vanders Ice Lobe about 12,000 years ago. In the wake of this ice lobe retreat, melt waters trapped between highlands and a wall of ice, varied drastically in elevation and longevity. Glacial Lake Duluth submerged most of the Bayfield Peninsula and the islands. Deglaciation and rising land from the removal of the weight of ice, created new drainages lowering lake levels exposing the Apostle Islands and more of the Bayfield Peninsula.
Shaped and isolated by Lake Superior, the islands are home to regionally rare habitats. These habitats include old growth forests, clay bluff communities, sandstone communities, lagoonal and bog communities, and endangered dunal communities. The Wisconsin Department of Natural Resources Natural Heritage Inventory Program has designated unique Maritime Forest, Sandscape (includes beaches, sandspits, cuspate forelands, and tombolos), and Maritime Cliff State Natural Areas within the Lakeshore.