Non-game and minnow species, a population that is typical of warm-water rivers in southern Minnesota, dominate the Little Cottonwood River. Common species include the Brassy Minnow, Emerald Shiner, Fantail Darter, Johnny Darter, Black Bullhead, Yellow Bullhead, Rock Bass, Slender Darter, Spotfin Shiner, Mad Tom, and Golden Redhorse.

Historically, the middle portions of the watershed provided moderate to excellent habitat for northern pike spawning. Notes from the 1950s tell that the lower reaches contained trout because of the nearby groundwater springs. In the lower portion of the river, game fish such as Walleye Pike, Channel Catfish, Northern Pike, and Smallmouth Bass can be found.

The Department of Natural Resources performed fish surveys in 1986 and 2000 and found 28 species in the Little Cottonwood River (Fish species list, Fish survey location map). Next