The park is 340 acres (140 ha) in size. It encompasses the cliff, plunge basin and gorge of the ancient waterfall, and a number of secondary ravines and basins. The lake (Glacier or Green lake) is 10 acres (4 ha) in size and 62 feet (20 m) deep. It is one of the few meromictic lakes in the US. The surrounding limestone cliffs are 180 feet (60 m) high.
Around 10 000 years ago, toward the end of the Wisconsin glaciation, the retreating ice sheet blocked the northern ends of the Onondaga and Butternut valley, forming long glacier lakes. The waterfall was formed when the glacier lake in the current Valley area south of Syracuse drained eastward to the Butternut valley. It has been estimated that the waterfall contained a volume of water greater than the American Falls at Niagara, and that the water flowed for a 2000 year long period. Green Lake occupies the plunge pool of the former waterfall. When the ice retreated further northward, a lower-lying channel (Rock-cut channel) was carved where the interstate 481 is currently located. This led the water flow to cease through Clark Reservation.
Clark Reservation sits astride one of the numerous "Syracuse channels" left by the last ice age, and is perhaps the most dramatic feature. Pumpkin Hollow, about to the east, was carved by similar west-to-east water flows, as were Smoky Hollow (1 mile south of Clark Reservation) and the gorge at Green Lakes State Park.