The biophysical history of the Short Hills site has been dominated by significant glacial processes, which have acted to alter the landscape. Over one million years ago a river system flowed north out of present day Lake Erie into what is now Lake Ontario. As water flowed over the escarpment, a gorge was created which recessed southward. The periods of glaciation that followed played the largest role in the creation of the current landscape. Glaciers scoured the surface, widening the valleys, and as they retreated they deposited a great deal of sand, gravel and clay. During the Wisconsin Ice Age (12,800 to 12,700 years ago), the area of Short Hills was flooded by the body of water known as Lake Warren. Glacial deposits then filled the lake, essentially burying the pre-existing gorge to 150 metres above sea level. The full retreat of the bodies of water that existed in the area left behind a network of streams flowing from south to north. These streams cut through the deposited materials, forming river valleys and various waterfalls.

Over time, the water levels in Lake Ontario lowered, resulting in the down cutting of streams and the further erosion of the landscape. Certain materials on the surface were left, forming the "Short Hills". Following the leveling of Lake Ontario water, the severe erosional activity in the area sharply declined. This brought about a return of vegetation and ultimately resulted in the landscape establishing its current state.