It flows west-southwest for about a mile before turning northwest, leaving behind Montour Ridge and entering a much larger valley.

Some distance after crossing Pennsylvania Route 45, it begins meandering west-southwest for several tenths of a mile before turning northwest.

[1] Beaver Run joins Chillisquaque Creek 7.8 miles (12.6 km) upstream of its mouth.

[6] Beaver Run was entered into the Geographic Names Information System on August 2, 1979.

A steel stringer/multi-beam or girder bridge carrying State Route 3003 was built over the stream in 1909 and repaired in 1973.

A concrete slab bridge was constructed over the stream in 1941 and repaired in 2007, 2 miles (3.2 km) northwest of Mooresburg.

A concrete culvert bridge carrying T-843 was built across the stream in the same year, is 24.0 feet (7.3 m) long, and is 1.6 miles (2.6 km) southeast of Potts Grove.

According to the Montour County Natural Areas Inventory, planting native trees along the stream in these reaches would reduce nonpoint source pollution and raise water quality.