A sensitive, rare area saturated by groundwater seepage makes up the nine-acre Fen Natural Area. Part of the park is included in the 7,028-acre St. Francois Mountains Natural Area. This, the state's largest natural area, has been given this designation in recognition of its outstanding natural and geologic features. More than 900 species of plants, some rare, have been recorded in Johnson's Shut-Ins State Park. Natural communities can be found in bottomland woods, upland ridges, bluffs and fens.
Glades also occur in the wild areas.
These rocky openings in the forests support drought-adapted plants and animals commonly found in deserts of the southwestern United States, such as prickly pear cacti and scorpions. The unusual eastern collared lizard, when disturbed, will stand upright and run on its hind legs. The East Fork Black River offers fishermen the opportunity to hook smallmouth and largemouth bass, bluegill and goggle eye. Picnic sites, playground equipment and an open shelter, which can be reserved in advance, make the park a great place for family gatherings. Johnson's Shut-Ins State Park offers overnight guests both basic and electric campsites.