The flow processes of drain from the north and south gates of the Isahaya reclamation dike and its contribution on salinity stratification in Isahaya Bay have been investigated by using a 3-D flow simulation model. The low salinity water mass by the drain is seen in the inner area of Isahaya Bay. It spreads thinly to the central area of Isahaya Bay and flows out to the Ariake Sea along the Shimabara Peninsula in about one tidal cycle. In a flood period, the freshwater from the drain gates decreased the average salinity in Isahaya Bay by about 0.6 PSU. On the other hand, the inflow of low salinity water from the Ariake Sea caused the decrease of about 8 PSU. The inflow of low salinity water from the Ariake Sea plays a dominant role in the salinity stratification in Isahaya Bay.
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