The behavior prediction of PAHs in Jinhae Bay using a three-dimensional ecological model(EMT-3D) was examined. A three-dimensional ecological model(EMT-3D) was applied to the simulation of PAHs behaviors in Jinhae Bay of Korea. The computed results of simulation were in good agreement with the observed values. The result of sensitivity analysis showed that photolysis coefficient and extinction coefficient were important factors in the variation of dissolved PAHs, and POC partition coefficient was important factor in the variation of PAHs in particulate organic matter. In the case of PAHs in phytoplankton, bioconcentration factor of plankton was the most significant and the most effective in all. In simulations of 30%, 50% and 80% reduction in total loads of PAHs, the concentrations of dissolved PAHs were shown to be lower than 24 ng/L, 20 ng/L and 16 ng/L, respectively.