A mathematical model was developed for predicting the daily variation in water quality of Toisigawara-ike, which is a small agricultural pond in Sasaguri Town, Fukuoka Prefecture, Japan. This model took into consideration the ecosystem's processes. In the modeling, the interactions among the three water quality indices of NOx-N, NH_4 -N, and Org-N were described by first-order kinetics. The model parameters were determined by referring to previous literatures and by conducting trial-and-error optimizations. The results indicated that the ecosystem model could successfully reproduce the daily variation in reservoir water quality despite its relatively simple model structure. Next, we investigated the issue of total nitrogen concentration because this value in the pond was much higher than the Japanese water quality standard required for paddy irrigation. In order to reduce the total nitrogen level in this pond to the level of paddy irrigattion, we examined how much the inflow load should be reduced based on the scenario analyses using the ecosystem model. The results indicated that it was necessary to reduce the current inflow load of nitrogen by 60% or more.