Two to five hundred million years ago material was deposited in the bottom of shallow seas which intermittently covered large portions of North America. As the deposits increased in thickness, the layers on the bottom were compressed to form limestone, shale, and sandstone. Today in the park, these rocks are 1300 feet above the sea. They are an important factor in the development of the terrain which exists now.

The park exhibits many karst features including one of the most outstanding karst features in the state, Mystery Cave. The cave is a maze of linear corridors. Over twelve miles of passage exist in two rock layers with strikingly different compositions. During dry years, the entire South Branch Root River sinks into the cave through gravel-filled crevices in the river bottom.