Muddy Run is a 12.6-mile-long (20.3 km)[1] tributary of the Conodoguinet Creek in Franklin County, Pennsylvania in the United States.
The 4.4-mile-long (7.1 km)[1] tributary Rowe Run joins Muddy Run southeast of Orrstown.
The 5.3-mile-long (8.5 km)[1] tributary Lehman Run joins the Muddy Run near Pleasant Hall, Pennsylvania.
The headwaters begin in the Letterkenny Army Depot. Muddy Run joins the Conodoguinet near Orrstown.
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