It originates at Notch Lake, near the Devil's Tombstone Campsite, and flows through the small villages of Edgewood and Lanesville, entering Ulster County at Chichester.

The water, in turn, started running down through an already gouged-out pass, forming a small river.

The United States Geological Survey (USGS) maintains stream gauges along Stony Clove Creek.

The station in Chichester in operation since 1997, 1.8 miles (2.9 km) upstream from the Esopus, had a maximum discharge of 14,300 cubic feet (400 m3) per second on August 28, 2011, as Hurricane Irene passed through the area.

The maximum daily SSC mean was 2,860 mg/L on December 1, 2010, and the minimum was under 1 mg/L over many days in late August through September 2014.