Non production in Ariake Bay was severely damaged by a bloom of diatoms in FY2000. Environmental changes which occurred in this bay were analyzed using data collected at 22 stations in the coastal area of Kumamoto, Japan from FY1995 to FY2000. Decrease in dissolved inorganic nitrogen (DIN) with increase of chlorophyll a (Chl-a) was observed in the latter half of the crop producing season in FY2000. Although the seawater temperature in FY2000 was slightly lower than that in FY1995-1999, no difference was detected in salinity. This suggests that temperature and salinity may not be the major parameters affecting the physiologies of layer and phytoplankton. On the other hand, the decrease in DIN for four years after construction of the dike at the mouth of Isahaya Bay had statistically significant effect on the physiologies of lava and phytoplankton for the six years. Variation in Secchi disk depth was not appeared in the six years but the increase in Secchi disk depth was significant after construction of the dike. This implies that the change of the ecosystem in Ariake Bay could have been induced by the artificial topographical change accompanied by construction of the dike in addition to some long-term environmental changes such as tide variation.