Muddy Run is a tributary of the West Branch Susquehanna River in Northumberland County, Pennsylvania, in the United States. It is 5.4 miles (8.7 km) in length. The creek is several miles northeast of the community of Milton. Main land uses include agricultural land and forest. The area of the creek's watershed is 11.4 square miles (30 km2), most of which is agricultural land. Muddy Run is entirely within Turbot Township. Most of the rock in the watershed is shale. The most common soil series is the Berks-Weikert-Bedington series.