We have been attempting to develop the numerical model for mercury fate in Minamata Bay and Yatsushiro Sea. In this paper we compared numerical results of bottom sediment transport from the bay to the outer sea area for one year with and without sea water and freshwater stratification. As a result, it was clarified that long term bottom sediment transport was determined by both of barotropic currents and baroclinic ones. Thus, accurate numerical model for particulate mercury fate must take into account baroclinic structure in actual coastal area due to freshwater inflow.
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