The Le Sueur River Watershed is one of the twelve major watersheds in the Minnesota River Basin. The Watershed is located in south central Minnesota within Blue Earth, Faribault, Freeborn, Le Sueur, Steele and Waseca counties. There are 20 municipalities in the watershed of which the City of Waseca is the largest. The Le Sueur River drains approximately 711,838 acres and meets the Blue Earth River at McGowan's Farm.

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There is concern over the resources in the Le Sueur River Watershed because of the topography, agriculturally dominated landscape, and increased development pressure in the region. As a result, there has been raised awareness over the quality of the surface and ground water, along with management of wetlands, drainage, nutrients, waste and stormwater. Recent findings have indicated the Le Sueur River is a major contributor of sediment and nutrients to the Minnesota River.