Elk Run is considered to be impaired by atmospheric deposition for a portion of its length.

It flows southeast for a short distance before entering a deep valley and receiving an unnamed tributary from the left.

After a short distance, the stream reaches its confluence with West Branch Fishing Creek.

[1] Elk Run joins West Branch Fishing Creek 3.64 miles (5.86 km) upstream of its mouth.

[3] A total of 0.43 miles (0.69 km) of Elk Run and its unnamed tributaries are considered to be impaired.

Bedrock consisting of sandstone and shale lines the slopes of the stream's valley.

[8] During the late Wisconsin glaciation, the location of the headwaters of Elk Run were at the glacial terminus on the northern part of North Mountain.

[3] The stream is entirely within the United States Geological Survey quadrangle of Elk Grove.

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

[9] Wild trout naturally reproduce in Elk Run between its headwaters and its mouth.

[14] A forest community along Elk Run is considered by the Sullivan County Natural Areas Inventory to be "locally significant".

However, there are smaller numbers of basswood, beech, hemlock, white ash, and yellow birch.

The shrub layer of the forest is described as "well-developed" in the Sullivan County Natural Areas Inventory.

Herbaceous plants in the area include asters, Christmas ferns, foamflowers, wood sorrels, and others.