The rugged hills and deep gorges of this preserve are covered with scattered stands of evergreens mixed with hardwood trees. White pine, hemlock, and Canada yew are relics which have persisted since the period following the last glacier when the climate was much colder. Both white pine and hemlock trees appear to be successfully reproducing.

The bedrock of Shades State Park was formed from sediments deposited when the area was covered by a vast inland sea. The deep ravines were formed much later. After the last glaciers receded northward, streams swollen with glacial meltwater cut into the bedrock. The four narrow ridges called backbones, which were left between stream curves, stand 70 to 100 feet above the valley. They are recognized as one of the most remarkable examples of incised meanders in the eastern United States.

Pine Hills was originally divided into a number of ownerships. One of the wider ridges adjoining the more level upland was cleared, but the rest of the land remained essentially in timber. A sawmill was set up in the 1850s as an addition to the Deer and Canine grist mill at Pine Bluffs. Timber cutting removed many of the larger hardwoods, but the pines and hemlocks were not seriously disturbed.

In 1868 the Pine Hill Woolen Mill Company placed a dam in Clifty Creek and cut a notch through the abutting hill. The impounded water ran through this open cut into a wooden flume connected with a water wheel that powered the mill. Due to damage from floods, the mill was removed to nearby Pine Bluff in 1873. Thus, the valley and surrounding hills were allowed to return to their original beauty.

The Indiana Chapter of The Nature Conservancy, a non-profit organization, raised money through private donations to acquire Pine Hills. It was conveyed to the Department of Natural Resources in October of 1961and became Indiana’s first state dedicated nature preserve. An additional 12 acres bordering Sugar Creek was contributed by Wabash College in 1971.