A system for water quality management in semi-enclosed bays is proposed. The system consists of water pipes from the open sea through an inner bay and water gates which can control the water level for effective transportations of the water. Flow rate of water is a critical parameter to maximize efficiency of the system
for water quality improvement and the dependency of the rate on such factors is examined as tidal range, length and size of cross section of the water pipes. As a preliminary study, a box model is used to evaluate the efficiency of the system for water purifications in the Hakata bay. Numerical results show that annually averaged COD values in the inner bay area are estimated as 40-60% of the existing values with 7 to 13% increases of outward flux of COD through the bay mouth.