Windom is a city in Cottonwood County, Minnesota. As of the 2000 census, the city had a total population of 4,490. It is the county seat of Cottonwood County6.
According to the United States Census Bureau, the city has a total area of 9.7 km2 (3.7 mi2). 9.2 km2 (3.5 mi2) of it is land and 0.5 km2 (0.2 mi2) of it is water. The total area is 5.08% water.