This study analyzed changes in hydrology between two recent decades (1980s and 2010s) with the Soil and Water Assessment Tool (SWAT) in three representative watersheds in South Dakota: Bad River, Skunk Creek, and Upper Big Sioux River watersheds. Two SWAT models were created over two discrete time periods (1981‐1990 and 2005‐2014) for each watershed. National Land Cover Datasets 1992 and 2011 were, respectively, ingested into 1981‐1990 and 2005‐2014 models, along with corresponding weather data, to enable comparison of annual and seasonal runoff, soil water content, evapotranspiration (ET), water yield, and percolation between these two decades. Simulation results based on the calibrated models showed that surface runoff, soil water content, water yield, and percolation increased in all three watersheds. Elevated ET was also apparent, except in Skunk Creek watershed. Differences in annual water balance components appeared to follow changes in land use more closely than variation in precipitation amounts, although seasonal variation in precipitation was reflected in seasonal surface runoff. Subbasin‐scale spatial analyses revealed noticeable increases in water balance components mostly in downstream parts of Bad River and Skunk Creek watersheds, and the western part of Upper Big Sioux River watershed. Results presented in this study provide some insight into recent changes in hydrological processes in South Dakota watersheds. Editor's note: This paper is part of the featured series on SWAT Applications for Emerging Hydrologic and Water Quality Challenges. See the February 2017 issue for the introduction and background to the series.