Water quality monitoring at Blair Gap Run, a high quality mountain stream, is an ongoing process at Allegheny Portage Railroad NHS. A group of local Senior Ranger volunteers test park waters for levels of specific conductance, total alkalinity, nitrates, phosphates, sulfates, and pH on a monthly basis.

While the waters of Blair Gap Run are clean, the Little Conemaugh River at the Staple Bend Tunnel unit of Allegheny Portage Railroad NHS has been polluted by acid mine drainage. Some sources of the mine drainage are located on park property, while others are located on adjacent properties, but flow through the park. However, steps have been made in the direction of treating the polluted waters flowing on the park property.