The Great Lakes Shipwreck Museum is located at the Whitefish Point Light Station 11 miles (18 km) north of Paradise in Chippewa County in the U.S. state of Michigan. The light station property was transferred to the Great Lakes Shipwreck Historical Society (GLSHS), the Michigan Audubon Society (MAS), and the United States Fish and Wildlife Service (USFWS) in 1996. The three entities share governance of the site. The museum is operated by the GLSHS. The museum exhibits artifacts from shipwrecks from the Whitefish Point Underwater Preserve and the bell from the wreck of the SS Edmund Fitzgerald. Admission to the museum includes a tour of historic buildings with displays that interpret the Great Lakes maritime, United States Coast Guard, and US Life-Saving Service history.

An active navigational light has operated at Whitefish Point since 1848. The United States Coast Guard (USCG) stationed personnel at Whitefish Point until 1971 when the navigational equipment was automated. Whitefish Township was successful in its bid to place the Whitefish Point light, the oldest active light on Lake Superior, on National Register of Historic Places in 1973.

The MAS secured a license from the Coast Guard in 1976 for access to the Whitefish Point Light Station property for the study of migrating birds. In 1978, the Whitefish Point Bird Observatory (WPBO) was formed as an affiliate of the MAS and began monitoring migrating birds at Whitefish Point.

The GLSHS was formed by a group of divers in 1978 as a private, nonprofit organization. Its mission is "to promote and augment an understanding and appreciation of maritime history with particular emphasis on the Great Lakes museum facilities." In 1983, the GLSHS obtained a 25-year lease from the United States Coast Guard (USCG) to operate a museum at the Whitefish Point Light Station. The GLSHS began obtaining public funds in 1984 from federal and state agencies.

In 1990, the GLSHS signed an agreement with Whitefish Township that gave residents and visitors public access to Lake Superior, parking, and the restrooms at Whitefish Point.

In 1992, the state of Michigan filed a lawsuit against the GLSHS for removal of artifacts from shipwrecks on the Great Lakes bottomlands in violation of Michigan's Antiquities Act of 1980. The Michigan Department of Natural Resources (DNR) obtained a search warrant in 1992 and raided the GLSHS offices and museum and found evidence that GLSHS had "removed about 150 artifacts from wrecks located on state-claimed bottomlands." In 1993, the state reached a settlement agreement with the GLSHS that loaned the artifacts back to them for display in the Great Lakes Shipwreck Museum.

In 1992, the stakeholders at the former Whitefish Point Light Station developed the Whitefish Point Comprehensive Plan. The stakeholders included Whitefish Township, the MAS, DNR, GLSHS, and USCG. The plan was developed with the purpose of discussion of land transfer of the Whitefish Point Light Station from the USCG and "proper land usage in terms of existing and future developments... to ensure that, through proper planning, the unique but somewhat fragile environment of the Coast Guard Site is fully protected."

In 1993, the GLSHS announced their intentions to seek a legislative transfer from the USCG so that they could hold 3 acres (1.2 ha) of the 44 acres (18 ha) of the Whitefish Point Light Station. In 1994, the GLSHS was involved in the removal of trees and the construction of an overflow parking lot. This led to a public meeting that discussed concerns about overdevelopment of the former light station.