Carbon Run is a tributary of Shamokin Creek in Northumberland County, Pennsylvania, in the United States.

Carbon Run is impaired due to metals from acid mine drainage, which colors the stream orange.

Much of the area in the vicinity of the stream consists of spoil piles and abandoned mining land.

In this reach, it enters Coal Township, receives two unnamed tributaries from the left, and passes through two small lakes.

The stream flows alongside Pennsylvania Route 125 for several tenths of a mile before turning north and entering Shamokin.

Several tenths of a mile further downstream, it turns northwest and reaches its confluence with Shamokin Creek.

[1] Carbon Run joins Shamokin Creek 21.62 miles (34.79 km) upstream of its mouth.

[6] The concentration of manganese and iron in Carbon Run at site CAR1 are 2.6 and 14.6 milligrams per liter (0.0026 and 0.0146 oz/cu ft), while the daily loads of these substances are 117.7 and 672.0 pounds (53.4 and 304.8 kg).

[4] The concentrations of recoverable sodium and potassium in Carbon Run at Shamokin were once measured to be 5.5 and 2.4 milligrams per liter (0.0055 and 0.0024 oz/cu ft).

[7] In 1999 and 2000, the instantaneous discharge of Carbon Run at Shamokin ranged from 3.2 to 18 cubic feet per second (0.091 to 0.510 m3/s) during three measurements.

In some reaches, the stream flows underground due to infiltration into mine pools, but returns to the surface in the form of a discharge.

They have helped to reduce the stream's acidity and made it able to support aquatic plant and animal life.

[8] A concrete stringer/multi-beam or girder bridge carrying Willow Street over Carbon Run in Shamokin was built in 1935 and is 26.9 feet (8.2 m) long.

A concrete culvert bridge carrying Spruce Street over Carbon Run was built in Shamokin in 1992 and is 25.9 feet (7.9 m) long.

[13] Masonry retaining walls were built on Carbon Run during the Great Depression.

[15] The Pennsylvania Department of Conservation and Natural Resources has awarded a $353,000 grant for stream improvements to Carbon Run.

[17] Non-motorized activities, such as hiking and horseback riding are banned in the area, but there are future plans to accommodate them.

[20] Macroinvertebrates began to repopulate Carbon Run by the 2000s due to the passive treatment systems in the watershed.

A small unnamed tributary to Carbon Run hosted various caddisflies, mayflies, stoneflies, and minnows.