Cherry Run is a small unincorporated community hamlet located along the CSX Transportation mainline on the Potomac River in Morgan County in the U.S. state of West Virginia. The community is named for the stream, Cherry Run, that meets the Potomac in its vicinity. It was originally known as Cherry Run Depot because of the important interchange between …Cherry Run is a small unincorporated community hamlet located along the CSX Transportation mainline on the Potomac River in Morgan County in the U.S. state of West Virginia. The community is named for the stream, Cherry Run, that meets the Potomac in its vicinity. It was originally known as Cherry Run Depot because of the important interchange between the B&O and the Western Maryland Railway located there.