The stream is acidic and is considered by the Pennsylvania Department of Environmental Protection to be impaired by atmospheric deposition.

The stream's pH during average flow conditions is 5.76 and the concentration of aluminum is 0.107 milligrams per liter.

[4] A total of 1.69 miles (2.72 km) of Shanty Run are considered by the Pennsylvania Department of Environmental Protection to be impaired due to atmospheric deposition caused by the stream's pH.

0.30 miles (0.48 km) of Shanty Run's unnamed tributary experience the same impairment.

[1] The lower reaches of Shanty Run are on rock of the Huntley Mountain Formation.

[4] Shanty Run flows over soil of the Deep-Wellsboro-Oquaga association in its lower reaches.

[4] Shanty Run and its unnamed tributary were first listed by the Pennsylvania Department of Environmental Protection as impaired in 2002.