Mugser Run is a 8.0-mile-long (12.9 km) stream in Columbia County, Pennsylvania, in the United States. It is a tributary of South Branch Roaring Creek. Mugser Run is located in Locust and Cleveland Townships. Forested land and agricultural land are by far the most common uses of land in the watershed. Brown trout and rainbow trout are found in the creek. The main rock formations are the Trimmers Rock Formation and the Catskill Formation–Buddys Run formation.
Mugser Run starts in near Pennsylvania Route 42 in Locust Township, between Numidia and Little Mountain. The creek flows west into Cleveland Township after a short distance. Upon entering Cleveland Township, it turns south and briefly skirts the northern edge of Little Mountain before turning north again. It passes by the community of Fisherdale and turns west, then turns north. For a while, the creek flows into a deep and narrow river valley. The valley widens out as the creek passes by a covered bridge. Just before its mouth, it passes by Knoebels Amusement Resort. The creek empties into South Branch Roaring Creek at the Northumberland County line.
Mugser Run has at least one tributary.
Forested land is the largest land use in the Mugser Run watershed, with 50.24% of the watershed consisting of forests. 45.65% of the land in the watershed of Mugser Run is devoted to agriculture. The third-largest use of land in the watershed is developed land, which takes up 4.11% of the watershed.
The southern edge of the Mugser Run watershed is on Little Mountain and the northern edge is in the rolling hills of Cleveland Township. The western edge is in Locust Township and the eastern edge is at the Columbia/Northumberland County line.
The area of the Mugser Run watershed is 11.9 square miles.