The Mukwonago River is one of the cleanest and most biologically diverse streams in southeastern Wisconsin.
[1] Ten of the eleven Sunfish found in Wisconsin are present in the river including the threatened Northern Sunfish.
In addition, the river is also home to a high biodiversity of waterfowl, reptiles, amphibians, insects, aquatic plants, and other wetland life.
It holds one of the last and largest strands of wild rice in Southeastern Wisconsin.
[4] Some of the invasive species that have been introduced to the watershed are the Asiatic Clam (Corbicula fluminea), Zebra Mussel (Dreissena polymorpha), Purple loosestrife (Lythrum salicaria), Eurasian Water-milfoil (Myriophyllum spicatum), and Curly-leaf pondweed (Potamogeton crispus).