The original fossil site, located along Highway 20 in Republic Ferry County, was first discovered in 1977 by artist Wesley "Wes" Wehr and paleontologist Kirk Johnson, than a high school student from Seattle.

While Perry had initially cautioned that the project was possibly impossible due to resources, she had been given support and training in paleobotany by Wehr on a trip to the Burke Museum in Seattle.

The center officially opened in August of that year as a proposed addition to the city parks department, with the name "Stonerose" being chosen as a reference to the rose family fossils found in the stones.

A 1988 Washington State Department of Community Development grant was given allowing for the formation of the non=profit organization Friends of Stonerose fossils as a support group for the center in 1989.

Through fund raising efforts such as "bingo bashes" the Friends of Stonerose fossils purchased over 10 city blocks of land surrounding and including the "Boot Hill" site, which itself had around 100 ft (30 m) of exposed strata.

[5] In 2019 the center again prepared for the possibility of moving locations, with fundraising to purchase a 4,000 sq ft (370 m2) building on Clark Avenue, the city main street.

The lake bottom layers are composed of volcanic ash which hardened into sedimentary rock, becoming fine-grained tuffaceous shales of the Klondike Mountain Formation.