The Raystown Branch of the Juniata River is the main drainage in the northern two-thirds of the county. The river flows to the east through the mountains within the county through several water gaps caused by a group of faults trending east–west through the central part of the county. The river then turns north and flows into Raystown Lake in Huntingdon County. The southern third of the county is drained by several tributaries of the Potomac River. Both the Potomac and Juniata rivers are part of the Chesapeake Bay Watershed.