This study established a 3D ecosystem model composed of stratification considering the topographic heat accumulation effect and river outflow, and then applied this model to Jinhae, Masan Bay. Specifically, it reenacted the formation and developmental process of ODW according to the stratification by calculating the kinematic eddy viscosity and eddy diffusion coefficient of the stratification model. The results were used as input data for the ecosystem model and compared with DO, COD, I-N, and I-P, which is the standard index of ocean water quality. As a result, it was determined that COD and T-N are third grade and T-P is second grade standards for a natural environment.