The museum was founded in Gills Rock, Wisconsin, in 1969 and began operating at the Cana Island Light in 1971.

[2] In 1993, the museum began a capital campaign to build a year-round facility in Sturgeon Bay, which was accomplished in 1997.

The site also hosts the tugboat John Purves, which was built in 1919, served the U.S. Army in World War II, and later sailed on the Great Lakes.

[5] Exterior construction was finished by November 5th, with the Jim Kress Lighthouse Tower becoming Sturgeon Bay's tallest building.

After the winter of 2015–16, heavy snow, rain, and decreased evaporation caused Lakes Michigan and Huron to rise 30+ inches; that summer the causeway was occasionally covered by water, so the Museum purchased a tractor and wagon to take visitors to the lighthouse when the causeway was covered with water.

Restoration as of summer 2018:Phase 1 has been completed and included new restroom facilities and a maintenance building; a parking lot; repair to the copper roof; repainting of the tower; repaired masonry on the tower and keeper's house; restoration of windows and doors; and many other updates.