The objectives of this study were to develop a linked watershed-waterbody modeling system and to assess the impacts of indirect wastewater reuse on irrigation water quality. The Osan stream watershed within Gyeonggi-do of South Korea was selected for this study. The linked modeling system was composed of the SWAT (Soil and water assessment tool) and QUALKO2 models. The SWAT model was calibrated and validated using the stream discharge and water quality data from 2010 to 2011. Runoff and non-point source pollutants from each subbasin and stream discharge from 1980 to 2009 were simulated by the SWAT model and applied to the QUALKO2 model. The QUALKO2 model was calibrated and validated under the conditions of low water and normal discharges, respectively. Finally, The 10-day irrigation water quality from April to September was simulated. The statistical measures of coefficient of determination ($R^2$), reliability index (RI), and efficiency index (EI) were used to evaluate the system performance. The $R^2$, RI and EI values ranged from 0.5 to 1.0, 1.03 to 1.92, and -35.03 to 0.95, respectively. The 10-day irrigation water quality showed the concentrations of BOD and coliform exceeded the water quality guidelines for wastewater reuse. The linked modeling system can be a useful tool to estimate non-point source pollutant loads in watershed and to control the water quality of effluent from a wastewater treatment plant and irrigation water in the downstream waterbody.