Beaver Run begins in eastern Lewis Township, Northumberland County. It flows southeast for a short distance before turning southwest and then south. The stream then crosses Pennsylvania Route 44 and Pennsylvania Route 54 before crossing a Conrail railroad and turning southeast. It flows in this direction for some distance before passing by the community of Schuyler and leaving Lewis Township. Upon leaving Lewis Township, Beaver Run enters Limestone Township, Montour County. Here it turns east for a short distance and then turns southeast. The stream then crosses a set of railroad tracks and further downstream reaches its confluence with County Line Branch near the eastern border of Limestone Township.
Hydrology
Portions of Beaver Run and its tributaries are affected by siltation and organic enrichment due to agriculture. The entirety of the stream and its tributaries are listed as "not attaining" in the 305B Stream Listings. The water of Beaver Run is relatively warm. Beaver Run has low levels of dissolved oxygen.
Geography and geology
The watershed of Beaver Run is in the Appalachian Mountain section of the ridge and valleyphysiographic region. Most of Beaver Run and the area in its vicinity lies over rock of the Onondaga and Old Port Formation. However, the southern part of the watershed is on rock of the Keyser and Tonoloway Formation and the upper reaches of the watershed, including some of the northern tributaries, lies over Hamilton Group rock. The soils in a small area in the lower reaches of the watershed of Beaver Run are of the Chenango-Pope-Holly soil series. The stream's southern tributaries and the rest of the lower and middle reaches of the watershed are on soil of the Hagerstown-Edom-Washington series. The upper reaches of the watershed lie over the Watson-Berks-Alvira soil series. Hydric soils also occur on the stream. Beaver Run is not influenced by limestone. The elevation of Beaver Run near its mouth is above sea level.
Watershed
Nearly all of the watershed of Beaver Run is agricultural land. However, there are some small patches of forested land. In addition to the townships that the stream flows through, the community of Turbotville is also in the watershed. There are of streams in the watershed of Beaver Run. The Beaver Run Bridge was built over Beaver Run in its lower reaches in 1915. It is a closed-spandrel arch bridge that is long. The bridge is open to traffic.
Biology
Beaver Run has been described as overgrown. The Montour County Natural Areas Inventory recommends planting native trees along the stream.
