Mud Run is a tributary of Green Creek in Columbia County, Pennsylvania, in the United States.

Mud Run begins in Greenwood Township on the western side of Bunker Hill.

It then turns east and flows parallel to the southern edge of the valley for a number of miles, receiving several unnamed tributaries on the way.

[3] Croplands are the largest source of sediment in the Mud Run watershed, contributing 3,299,200 pounds (1,496,500 kg) per year.

[3] The K-factor, a measure of inherent soil erodability of the Mud Run watershed is 0.3 for wetlands, 0.29 for cropland, 0.284 for hay and pastures, and 0.26 for forests.

The watershed's LS factor, which concerns slope steepness and length, is 4.705 in forests, 1.348 in hay and pastures.

The remainder of the land is designated as "low-intensity development" by the Pennsylvania Department of Environmental Protection (5.2%), or is a wetland (0.1%).

14.2 miles (22.9 km) of streams are considered by the Pennsylvania Department of Environmental Protection to be impaired.