The three-dimensional eco-hydrodynamic model was applied to estimate the autochthonous COD caused by production of phytoplankton in Jinhae Bay. A residual current was simulated, using a hydrodynamic model, to have a sightly complicated pattern in the inner part of the bay, ranging from 0.001 to 5 cm/s. In the outer part of the bay, the simulated current flowed out to the south sea with a southward flow at a maximum of 25 cm/s. The results of the ecological model simulation of COD levels showed high concentrations, exceeding 4 mg/L, in the inner bay of Masan, an area of wastewater discharge, and lower levels, approaching less than 1 mg/L, closer to the outer part of the bay. The simulation results of Autochthonous COD by two methods using ecological modeling, showed high ratio over 70% of total COD. Therefore, it is more important to consider nutrients than organic matters in the region for control COD standard.