Torrents of runoff at the end of the Wisconsin glaciation 10,000 years ago carved the bed of the Mississippi River down into this limestone, leaving high bluffs along its banks.

The park is situated in the Driftless Area, an atypically rugged region of the Upper Midwest because it was never glaciated and covered with a layer of glacial till, or drift.

These include several kinds of oak, maple, elm, cedar, and ash, as well as black walnut, hickory, basswood, ironwood, birch, and poplar.

Terrestrial species include white-tailed deer, coyotes, red foxes, opossums, and timber rattlesnakes.

A 1971 analysis recommended that John A. Latsch State Park be reclassified as a Scientific and Natural Area, though this has not been acted upon either.