Part of the stream is designated as an impaired waterbody due to sedimentation and siltation from grazing-related agriculture.

[2] A total of 2.6 miles (4.2 km) of streams in the watershed of Muddy Run are designated as impaired waterbodies.

In addition to sediment, Muddy Run is also affected by E. coli, nutrient pollution, and thermal radiation.

In the future, the nitrogen load could be reduced by 20.26 percent to 29,406 pounds (13,338 kg) per year.

In the future, the phosphorus load could be reduced by 37.53 percent to 839 pounds (381 kg) per year.

[4] In 2000, the total load of nitrogen in Muddy Run from groundwater was 14,221 pounds (6,451 kg).

[2] The mouth of the stream is in the United States Geological Survey quadrangle of Lewisburg.

A total of 227 acres (92 ha) of agricultural land in the watershed is on slopes of more than 3 percent.

[4] Muddy Run was entered into the Geographic Names Information System on August 2, 1979.

Armstrong Run is also the name referenced in the landowners and residents map published in 1868 by Pomeroy and Beers of Philadelphia.

A concrete stringer/multi-beam or girder bridge carrying State Route 1001 was constructed over Muddy Run in Mazeppa in 1932.