[2] The watershed of the stream has an area of 8.70 square miles (22.5 km2) and is in the Lower Susquehanna River drainage basin.

Logan Run begins on Shamokin Hill, near the southern border of Rush Township.

It flows west in a valley for a short distance before turning north for a few tenths of a mile.

At this point, the stream crosses State Route 2004 and turns northwest for a short distance.

At this point, the stream crosses Pennsylvania Route 54 and flows north for several tenths of a mile before reaching its confluence with the Susquehanna River.

[2] Logan Run joins the Susquehanna River 138.96 miles (223.63 km) upstream of its mouth.

[2] There are beds of rock containing rounded boulders on Logan Run at an elevation of 725 feet (221 m) above sea level.

[5] Sandstone of the Catskill Formation has been found in the hills in the vicinity of Logan Run.