Miller Run is a tributary of Limestone Run in Union County, Pennsylvania, in the United States. It is approximately 1.2 miles (1.9 km) long and flows through East Buffalo Township and Lewisburg. The watershed of the stream has an area of 0.87 square miles (2.3 km2). The stream has no officially named tributaries. It is very small and is not a perennial stream, but is impacted by stormwater flows and also has high concentrations of sediment. The stream's chemical hydrology has been significantly affected by human use. Major rock formations in its watershed include the Bloomsburg Formation, the Keyser-Tonoloway Formation, and the Wills Creek Formation.