The river begins in Windsor in northern Dane County and flows for a short distance in the town of Leeds in Columbia County, then returns to Dane County and flows southward through the villages of DeForest and Windsor, and the towns of Burke and Westport into Lake Mendota in the city of Madison.

Downstream from Lake Mendota, the river is channelized through the Madison Isthmus southeastward, and flows through Lake Monona, Lake Waubesa and Lake Kegonsa, passing through the city of Monona, the village of McFarland, the towns of Dunn and Pleasant Springs, the city of Stoughton and the town of Dunkirk (including the unincorporated community of Dunkirk) in Dane County; and the towns of Porter (including the unincorporated community of Stebbinsville) and Fulton (including the unincorporated community of Fulton) in northern Rock County.

It joins the Rock River in the town of Fulton, approximately 9 miles (14 km) northwest of Janesville.

According to the Geographic Names Information System, it has also been known historically as "Catfish River" (Sauk "Myan-mek", Potawatomi "Gooskehawn" [Gishkzhigwen], and Ho-Chunk "Gahara" [howį́ǧera]).

[1] During World War II, a U.S. Navy gasoline tanker, the USS Yahara (AOG-37), was named after the river.