The Kickapoo River is a gentle, meandering river flowing past diverse vegetation and alongside sandstone bluffs. Water quality of the Kickapoo has improved greatly over recent years. Fish studies have identified 31 species in the Kickapoo River. Water depth typically varies from less than one foot to three or four feet, yet some deep holes create a depth of over six feet. During spring thaws and after heavy rains, the Kickapoo River is known to rapidly go above flood stage ("Flash Flood"). At times, flood waters cover road and bridge surfaces. A U.S. Geological Survey water stage station at La Farge provides real time information of river flow conditions.

Five main tributaries feed the Kickapoo within the Reserve. Of these, Billings Creek, Weister Creek and Warner Creek have reputations as excellent streams for fishing brown trout, rainbow trout and brook trout. Organizations and agencies such as the Coulee Region Chapter of Trout Unlimited, U.S. Fish and Wildlife Service, Vernon County Land and Water Conservation, Wisconsin Department of Natural Resources, Natural Resource Conservation Service, and the Ho-Chunk Nation have made efforts in improving fish habitats and populations through stream restoration, surveys, and other related work.

Several small ponds exist in the Reserve. Whereas these do not support abundant fish populations, the ponds do provide valuable habitat for amphibians, reptiles, birds, and aquatic invertebrates in the Kickapoo Valley.