The hydrodynamics and water quality in Hakata Bay, Japan are strongly affected by the seasonal variations in both the gravitational circulation and the stratification in the bay. The three-dimensional hydrodynamics and water quality model has been developed to simulate the long-term transport and fate of pollutants in the system. The model is unique in that it completely integrates the refined modelling of the hydrodynamics, biochemical reactions and the ecosystem in the coastal waters. It is a 3-dimensional segmented model which is capable of resolving mean daily variations in all the parameters relevant to pollution control. It predicts daily fluctuations in the oxygen content at different depths in water throughout the year. It takes into account transport and settling of pollutant particles. It predicts light penetration from computed turbidity variations. It includes interactions between the ecosystem and water quality through nutrient cycling and photosynthesis. The model has been calibrated well against the data set of historical water quality observations in Hakata Bay.