The Central Wisconsin River Basin is a subset of the Wisconsin River corridor, located in Central Wisconsin. The basin is 4,021 square miles and is divided into 29 watersheds. Landuse in the basin is mixed with an abundance of forest as well as farm land. Agriculture in the basin includes cranberries, dairy, and irrigated potato/vegetable production in central sands.

Counties within the basin include most of Marathon, Wood, Portage, Juneau, and Adams, much of Monroe, and small parts of Waushara, Clark, Jackson and Vernon. Urban areas in the basin include Tomah, Stevens Point, Wisconsin Rapids, Marshfield, and Wausau.

The big natural resource issues in the basin are water quality and non-point pollution sources. Some segments in the watershed are on the 303d list of impaired waters. Other major issues include groundwater quality (atrazine, nitrates) and the groundwater-surface water interface. In addition to water resource issues, forest fragmentation is a major issue along with management of natural habitats.