Muddy Run may refer to:Muddy Run, a stream in New Castle County, Delaware Muddy Run, a stream in Fayette County, Pennsylvania Muddy Run, in Franklin County, Pennsylvania Muddy Run, a tributary of the Maurice River in New Jersey Muddy Run, in Northumberland County, Pennsylvania Muddy Run Pumped Storage Facility, a hydroelectric generation facility on the Susquehanna River in Pennsylvania Muddy Run, in Union County, Pennsylvania