Windom is a city in Cottonwood County, Minnesota, United States. The population was 4,646 at the 2010 census. It is the county seat of Cottonwood County and is situated in the Coteau des Prairies. Although it is a small, rural farming community, Windom is host to several parks including a disc golf course at Mayflower Park. The Des Moines River flows through Windom and serves as a gentle, rapid-free canoeing spot.