Muddy Run (Conodoguinet Creek tributary)

Muddy Run is a 12.6 mi tributary of the Conodoguinet Creek in Franklin County, Pennsylvania in the United States.

The 4.4 mi tributary Rowe Run joins Muddy Run southeast of Orrstown.

The 5.3 mi 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.