Multidimensional dynamic water quality model of organic matter and trophic state was applied to the Han River system. The model was calibrated using field measurement data obtained during the year of 2007. The model results showed reasonable performance in predicting temporal variations of TN, TP, Chl-a and BOD concentrations. The applied integrated modeling system can be effectively used to simulate water quality as well as hydrodynamic and water temperature for river-lake continuous system in the Han River. Utilizing the calibrated model, we analyzed the spatial and temporal distributions of TN, TP, Chl-a and BOD concentrations in the Han River system. The temporal variations of water quality at each river reach and lake were effectively simulated with the developed model and spatial distribution of water qualities in the Han River system could be compared. The multidimensional dynamic modeling system can simulate the water qualities of entire waterbody where Lake Paldang and the incoming flows are included using single modeling system. So it can be effectively used for integrated water quality management of the Han River system.