The Root River SWCD was formed in 1939, the third SWCD in the state, preceded by Burns-Homer-Pleasant and Gilmore Creek-Stockton-Rollingstone SWCDs.   At that time, Districts did not follow county geographic lines. Upon origination Root River SWCD encompassed all of Houston County and the eastern portion of Fillmore County. In 1941 a portion of Winona County also joined the Root River SWCD. During the 1960s the boundaries were revised, with the Fillmore County portion of the District merging with West Fillmore SWCD and leaving Root River SWCD with our present boundary.

The District formed for the reason that people living in the valleys were concerned about flooding.  In addition, upland users had problems with erosion causing ditches to form which resulted in lower yields on cropland.  These problems and concerns caused incomes to fall threatening survival of the family farm unit.  In many instances land users accepted conservation practices on the land as an alternative to abandoning the farm. The results of these practices were recognized and adopted by their neighbors. 

The founding supervisors of the District were Ed Albrecht, H. L. Sather, John Wheaton, Joseph Lorenz, and Frank Ormsby.

Technical assistance was provided to the District through the USDA.  It was modeled after the popular demonstration projects of the Civilian Conservation Corps (CCC) program, farmers received technical and financial assistance in treating the resource needs of their farm.