For a short distance, Hell Run flows in an entrenched channel. This channel was probably formerly a small cave through which the stream flowed. The angular bends of the stream here suggest that it follows fractures in the limestone. The weakness caused by the fractures probably resulted in the collapse of the thin roof rock, resulting in the channel we see today.
To see a small cave that is probably very similar to the one that collapsed to form the Flume, see the Caves and Natural Bridges along the Slippery Rock Gorge Trail.