Walker Run begins near State Route 4002 in Salem Township. It flows west-southwest for a few tenths of a mile before turning southwest, entering a valley and flowing alongside Stone Church Road. Over the next few miles, the stream gradually turns south-southeast. It then begins meandering southwest, receiving three unnamed tributaries. The stream eventually turns south-southeast and then south, crossing US Route 11. A short distance further downstream, it turns west for several hundred feet before turning south. It then almost immediately reaches its confluence with the Suquehanna River near the border between Salem Township and Nescopeck Township. Walker Run joins the Susquehanna River upstream of its mouth.
Tributaries
Walker Run has no named tributaries. However, it does have several unnamed tributaries. The first is approximately and joins Walker Run downstream of Summer Hill. The second is approximately long and joins Walker Run near the first tributary. The third tributary is approximately long.
Hydrology
The discharge of Walker Run at its mouth has a 10 percent chance of peaking at 660 cubic feet per second in any given year. It has a 2 percent chance of reaching 1600 cubic feet per second, a 1 percent chance of reaching 2200 cubic feet per second, and a 0.2 percent chance of reaching 3790 cubic feet per second. The stream has a 10 percent chance of peaking at 550 cubic feet per second upstream of Denns Road and a 2 percent chance of peaking at 1320 cubic feet per second there. It has a 1 percent chance of reaching 1860 cubic feet per second and a 0.2 percent chance of reaching 3100 cubic feet per second. Upstream of the North Market Street bridge, the stream has a 10 percent chance of peaking at 480 cubic feet per second and a 2 percent chance of peaking at 1180 cubic feet per second. It has a 1 percent chance of reaching 1640 cubic feet per second and a 0.2 percent chance of reaching 3600 cubic feet per second.
Geography and geology
The elevation near the mouth of Walker Run is above sea level. The elevation of the stream's source is between above sea level. Walker Run flows over rock of the Mahantango Formation in its lower reaches. Further upstream is a narrow band of the Harrell Formation. The stream's upper reaches are on much broader bands of the Irish Valley Member and the Trimmers Rock Formation. The Irish Valley Member contains sandstone, siltstone, claystone, and shale. The Trimmers Rock Formation contains sandstone, siltstone, silt shale, and silty clay shale. The Harrell Formation contains clay shale and silty clay shale and the Mahantango Formation contains claystone and limestone. All of these rock formations date to the Devonian Period. There are eleven features identified by the Federal Emergency Management Agency as obstructions on Walker Run. This is 44 percent of the 25 obstructions in Salem Township. There are pools on Walker Run near the bridge carrying North Market Street over the stream. These pools are surrounded by trees. Walker Run has surrounding wetlands in some places.
The entire drainage basin of Walker Run is designated as a Coldwater Fishery and a Migratory fishery. have discovered wild brown trout in the stream. The trout include fingerlings and several year classes.