This study presents a decision support method that can quantify the effects of water management practices on surface water and groundwater systems using a basin-scale fully-integrated model. For improvement to the decision-making process, the integrated model consists of evapotranspiration, surface, and subsurface hydrologic conditions and accounts for anthropogenic water management such as groundwater pumping, and dam and weir operations, which significantly affect the water resources of the Geum River Basin, South Korea. In this study, the fully-integrated model is calibrated based on a step-wise calibration approach. For a reliable decision support model, the calibrated model was further evaluated against five-year monthly transient agricultural pumping and control structure operation data with taking into account the parametric uncertainty of the model. The calibration and evaluation results agree well with various observation datasets including watertable depths, surface flow, reservoir water depths, and dam and weir discharge rates. Simulation results reveal that annual average net precipitation ratio for the simulation period is 0.32 with a range from 0.12 to 0.40, which is a water surplus condition. Within each year, however, negative net precipitation ratios, or water deficit conditions, occur consistently during the dry seasons, indicating that the hydrologic systems in the basin may be vulnerable during the dry seasons. Groundwater pumping within the basin lowers the local groundwater levels an average of 0.52 m over five years. In the downstream area of the basin, groundwater pumping activities affect approximately 30% of the area and result in a reduction of groundwater levels by 0.4 m with an acceptable range of uncertainty. As a decision support method for weir operations, we apply a weir removal scenario to evaluate the changes in surface flow conditions. The simulation results reveal that surface flow rates in weir reservoirs increase by three orders of magnitudes and surface water depths in the reservoirs of the dams and weirs reduce by two to four times compared to a case where all the weirs are in operation. Therefore, appropriate weir removal plans are necessary to minimize the impact on the ecosystem of the Geum River.