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The Mississippi River - St. Cloud Watershed covers 691,200 acres (1,080 square miles) in the south-central part of the Upper Mississippi River Basin. The watershed includes all or parts of the counties of Benton, Meeker, Mille Lacs, Morrison, Sherburne, Stearns, and Wright.

The Mississippi River - Winona Watershed covers 419,200 acres in the southeast Minnesota counties of Wabasha, Winona, and Olmsted. A majority of the watershed is cropland, with forest and grassland covering large portions as well.