The Cottonwood River (Dakota: Wáǧa Ožú Wakpá, lit.

It rises southwest of Balaton in Rock Lake Township in southern Lyon County, as an intermittent stream on the Coteau des Prairies, a morainic plateau dividing the Mississippi and Missouri River watersheds.

The largest is Sleepy Eye Creek, 51 miles (82 km) long, which flows eastwardly through Redwood and Brown Counties, past Cobden.

Tributaries from the south include Plum Creek, 35 miles (56 km) long, which flows northeastwardly through Murray and Redwood Counties, past Walnut Grove; and Dutch Charley Creek, 46 miles (74 km) long, which flows northeastwardly through Murray, Cottonwood, and Redwood Counties.

[3][6][7][8] Approximately 84% of land in the Cottonwood River watershed is used for agriculture; the predominant crops are corn and soybeans.