The water quality model for integrated water management in the Chikugo basin and the Ariake Sea is developed in this study. The integrated model is composed of three models: 1) the tank model; 2) the river model and 3) the two-dimensional box model of the Ariake Sea. Water quality parameters in this study are COD, SS and nutrient concentrations. Sensitivity analysis is carried out using the integrated model to evaluate the contribution of discharged loading from land area on water quality in the Ariake Sea from 1991 to 2000. It indicates that the nutrient concentrations in the vicinity of the mouth of the Chikugo River tend to increase during the period of high loading from the Chikugo basin while there is slightly effect of the discharged loading on COD and SS in the same area.