The Green and Nolin Rivers possess one of the most diverse fish (82 species) and invertebrate faunas (51 species of mussels) in North America. In addition to the mussels, there are approximately 200 species of benthic macroinvertebrates in these rivers. For these biological reasons, the Green River has been designated an "Outstanding Resource Water". As explained above, since Green River is the base-level stream for the Mammoth Cave System, it has crucial influence on the cave aquatic community since food supply and sediment transport are both affected.
Normal flow of 16 miles of the Green River, 7 miles of the Nolin River, and many miles of cave streams in the park is retarded by a relict dam known as Lock and Dam #6. Habitats for 7 federally listed endangered aquatic species are seriously degraded through reduction of natural flow velocity and resultant siltation. The quality of recreational non-motorized boating is also seriously diminished by the 21 miles of pooled river within the park.