Blair Gap Run is a high qulaity mountain stream running in and out of the park from the Cresson Mountain summit to Duncansville, PA. The headwaters originate at the Main Unit of the park near the Cresson Summit. The stream supports a cold water fishery further down the mountain near Muleshoe Curve.

At the Staple Bend Tunner unit of the park near Mineral Point, PA the park parallels the Little Conemaugh River. Intermittent streams and drainages flow through the park on their way to the river. Unfortunately, these are polluted by acidic abandoned mine drainage, which the park is working to remediate.