Allegheny Portage Railroad's Main Unit is located at the juncture of three Pennsylvania River Regions. To the north, headwaters of Bradley Run flow toward Clearfield and the West Branch of the Susquehanna River. To the east, the headwaters of Blair Gap Run eventually flow to the Juniata River. The third region, the Lower Allegheny and Monongahela Rivers, is fed by headwaters originating southwest of the park. Because the Allegheny Portage Railroad followed Blair Gap, that Run is the main stream located within the park.