Stony Run is a tributary of Little Catawissa Creek in Schuylkill County, Pennsylvania, in the United States.

Several tenths of a mile downstream, it crosses Ridge Road and turns east-southeast, almost immediately reaching its confluence with Little Catawissa Creek.

[1] Stony Run joins Little Catawissa Creek 1.96 miles (3.15 km) upstream of its mouth.

[2] At 1:00 P.M. on July 1, 1997, the air temperature in the vicinity of Stony Run 1.14 miles (1.83 km) upstream of its mouth was 26 °C (79 °F).

An area of land belonging to a Nature Conservancy Priority Forest Hub is located in the upper reaches of the watershed.

[2] Stony Run is in the United States Geological Survey quadrangles of Shumans, Nuremberg, Ashland, and Shenandoah.

[2] Stony Run is considered by the Pennsylvania Department of Environmental Protection to be a Coldwater Fishery.

The stream cannot support fish life due to the fact that it has been affected by acid precipitation.