The study was aimed to evaluate the applicability of a three-dimensional (3D) hydrodynamic and water quality model, ELCOM-CAEDYM for Yongdam Reservoir, Korea. The model was applied for the simulations of hydrodynamics, thermal stratification processes, stream density flow propagation, and water quality parameters including dissolved oxygen, nutrients, organic materials, and algal biomass (chl-a) for the period of June to December, 2006. The field data observed at four monitoring stations (ST1∼ST4) within the reservoir were used to validate the models performance. The model showed reasonable performance nevertheless low frequency boundary forcing data were provided, and well replicated the physical, chemical, and biological processes of the system. Simulated spatial and temporal variations of water temperature, nutrients, and chl-a concentrations were moderately consistent with the field observations. In particular, the model rationally reproduced the succession of different algal species; i.e., diatom dominant during spring and early summer, after then cyanobacteria dominant under warm and stratified conditions. ELCOM-CAEDYM is recommendable as a suitable coupled 3D hydrodynamic and water quality model that can be effectively used for the advanced water quality management of large stratified reservoirs in Korea.