The South Fork of the Little Conemaugh River flows through the park. Unfortunately, acidic mine drainage from the Saint Michael and Beaverdale areas pollutes the river, and it is fishless. Efforts are underway to remediate the mine pollution upstream of the park, which will improve the water quality within the park.

Although fishless, polluted rivers and streams are not lifeless. Some forms of bacteria and algae are adapted to acidic conditions. Pollution-tolerant insects and other animals can also inhabit polluted waterways.