The mountainous terrain of the Allegheny Mountain section of the Appalachian Plateau posed a problem to the Pennsylvania Mainline Canal, leading to the creation and use of incline planes that came to be known as the Allegheny Portage Railroad. The terrain-influenced form of transit, once novel and innovative for its time, is the backbone of the park’s history.

The Main Unit of Allegheny Portage Railroad NHS lies on a dividing ridge of the Allegheny Mountains that separates two major drainage basins: the Chesapeake Bay Watershed and the Ohio River basin. The headwaters to Blair Gap Run, which eventually flow to the Susquehanna River and the Chesapeake Bay, are found within the park. At the Staple Bend Tunnel Unit, seeps and intermittent streams are found along the historic railroad trace, which is now a hiking and biking trail. These flow into the Little Conemaugh River, which eventually joins the Ohio River.