The surficial geology in the vicinity of the stream's lower reaches mainly consists of Wisconsinan Till, bedrock, and Boulder Colluvium.

Green Run begins in a pond near Tooley Corners in Spring Brook Township.

It flows northwest for a few tenths of a mile and almost immediately enters Roaring Brook Township.

It flows generally in a westerly direction for a few miles in a deep valley near the border between Spring Brook Township and Scranton.

The stream eventually turns south-southwest for several tenths of a mile and reaches its confluence with Spring Brook.

[2] Green Run joins Spring Brook 6.48 miles (10.43 km) upstream of its mouth.

[1] Wild trout naturally reproduce in Green Run from its headwaters downstream to its mouth.

[13] The stream is also considered by the Pennsylvania Fish and Boat Commission to be Class A Wild Trout Waters from its headwaters downstream to its mouth.

[9] A large number of macroinvertebrate species have been observed in Green Run, including 16 genera in the orders Ephemeroptera, Plecoptera, and Trichoptera.