A mathmatical model was developed for precicting the daily variation of creek water quality in the flat low-lying paddy-cultivated area along the northern Ariake Sea during irrigation period by considering ecosystem processes in the creek water. In the modeling, the interactions among the five water quality indices of NOx-N, NH4-N, Org-N, PO4-P and Org-P were described by first-order kinetics. The model paraments were determined by referring the past literature together with the optimization using a simplegenetic algorithm with the ni situ measurements executed at a creek located in Anegawa, Kanzaki Town, Saga Prefecture, Japan. The relative sensitivities of model paraments were also calculated in order to identify the more important parameters for estimating the creek water quality. The results indicated that the ecosystem model was capable of successfully reproducing the daily variation of creek water quality despite its relatively simple model structure.