The Stockton-Rollingstone-Minnesota City Watershed District lies in the Buffalo Whitewater Watershed and is part of the Lower Mississippi River Basin. The District corresponds to the geographical extent of the Garvin Brook Watershed and lies entirely within Winona County.
The Stockton-Rollingstone-Minnesota City Watershed District itself consists of eleven minor watersheds. The major streams within the District are Garvin Brook, Stockton Valley Creek, and Rollingstone Creek. Stockton Valley Creek flows into Garvin Brooke just above Stockton. Garvin Brooke continues downstream until it converges with Rollingstone Creek above Minnesota City, before discharging into the Mississippi River within the Upper Mississippi River National Wildlife and Fish Refuge.