Chimneystack Run is a tributary of Coles Creek in Columbia County, Pennsylvania, in the United States. It is approximately 1.8 miles (2.9 km) long and flows through Sugarloaf Township. The watershed of the stream has an area of 1.07 square miles (2.8 km2). The stream's headwaters are located between Red Rock Mountain and Central Mountain. It has no named tributaries, but one unnamed tributary. Chimneystack Run is named after Chimneystack Rock. Wild trout inhabit the stream. Glaciation has affected the geography and geology in its vicinity.