Watershed health, including the natural environment, hydrology, water quality, and aquatic ecology, was assessed for the Han River basin (34 148 km<sup>2</sup>) in South Korea using the Soil and Water Assessment Tool (SWAT). The evaluation procedures followed those of the Healthy Watersheds Assessment by the U.S. Environmental Protection Agency (EPA). To evaluate watershed health (basin natural capacity), 6 components of the watershed landscape were examined: stream geomorphology, hydrology, water quality, aquatic habitat condition, and biological condition. In particular, for the hydrology and water quality components, the SWAT was applied for the study basin with 237 sub-watersheds (within a standard watershed on the Korea Hydrologic Unit Map) and including three multipurpose dams, one hydroelectric dam, and three multifunction weirs. The SWAT was calibrated (2005–2009) and validated (2010–2014) using each dam and weir operation, the flux tower evapotranspiration, TDR soil moisture, and groundwater level data for the hydrology assessment and using sediment, total phosphorus, and total nitrogen data for the water quality assessment. The water balance considering the surface–groundwater interactions and the variation in stream water quality were quantified according to the sub-watershed-scale relationship between the watershed hydrologic cycle and stream water quality. We assessed the integrated watershed health according to the U.S. EPA evaluation process based on the vulnerability levels of the natural environment, water resources, water quality, and ecosystem components. The results suggest that approaches aimed at simultaneously improving the water quality, hydrology, and aquatic ecology conditions may be necessary to improve integrated watershed health.