The Thompson Run Watershed is approximately 5.5 square miles in area. It is located in southern Allegheny County, about 11 miles southeast of Pittsburgh, Pennsylvania. Thompson Run can be accessed by taking State Highway 837 South from Pittsburgh about one third of a mile past Kennywood Amusement Park, where it crosses over Thompson Run near the confluence with the Monongahela River. ​Thompson Run is part of the Ohio River Basin in Allegheny County and drains directly into the Monongahela River. Its source is abandoned mine drainage.