Independence Run is a tributary of the Susquehanna River in Snyder County, Pennsylvania, in the United States.

The stream then turns east-southeast for several tenths of a mile, receiving one unnamed tributary from the left and one from the right.

[1] Independence Run joins the Susquehanna River 109.82 miles (176.74 km) upriver of its mouth.

However, planting trees along streambanks to create a riparian buffer would improve this, as well as connect forest habitats.

[6] In 2016, the Pennsylvania Fish and Boat Commission passed regulations affecting Independence Run from its mouth to a point 0.5 miles (0.80 km) upstream.