The following is a list of protected areas and preserves within the Great Lakes area.

• Alger Underwater Preserve
• Apostle Islands National Lakeshore
• Calumet Shoreline
• De Tour Passage Underwater Preserve
• Glenwood Shoreline
• Grand Traverse Bay Bottomland Preserve
• Fathom Five National Marine Park
• Indiana Dunes National Park
• Keweenau Underwater Preserve
• Lake Superior National Marine Conservation Area
• Manitou Passage Underwater Preserve
• Marquette Underwater Preserve
• Pictured Rocks National Lakeshore
• Sanilac Shores Underwater Preserve
• Sleeping Bear Dunes National Lakeshore
• Southwest Michigan Underwater Preserve
• Straits of Mackinac Shipwreck Preserve
• Thumb Area Bottomland Preserve
• Thunder Bay National Marine Sanctuary and Underwater Preserve
• Whitefish Point Underwater Preserve