As an effort to clarify the ecosystem of Osaka Bay, a semi-enclosed coastal area under the influence of stratification, a three-dimensional water quality model with combination of the baroclinic flow model and primitive eco-system model was constructed. The proposed model succeeded in simulating the time-depending flow and density structure and the baroclinic residual currents in Osaka Bay. In present study, we tried to improve the model by taking account of the benthic-pelagic interaction and exchange of nutrients between sea bottom sediments and overlaying water. On vertical structure, the model consists of 13 layers of water and eight layers of sediments. Long-term prediction of water quality was conducted from 1964 to 1985. This period is characterized by rapid water pollution and its decrease by the cutoff reduction of COD and P flowed into Osaka Bay. By combining the sediment model into original model, the numerical model was confirmed to shows more reasonable results in simulating the water quality in Osaka Bay.