Chimneystack Run begins in a deep valley between Central Mountain and Red Rock Mountain in northern Sugarloaf Township, slightly more than 1,000 feet (300 m) south of the Columbia County/Sullivan County line.

After a few tenths of a mile, it leaves its valley altogether, turning south-southeast and flowing down Central Mountain.

[2] Chimneystack Run joins Coles Creek 4.70 miles (7.56 km) upstream of its mouth.

The surface in these areas contains cobbles and boulders made of quartz, sandstone, and conglomerate.

In the stream's upper reaches, the bedrock contains red and gray sandstone and shale.

[3] The stream is entirely within the United States Geological Survey quadrangle of Red Rock.

[1] Chimneystack Run was entered into the Geographic Names Information System on August 2, 1979.