To conduct a scenario analyses for the improvement and preservation of water environment in an agricultural pond, a primary ecosystem model was developed for predicting the temporal fluctuation of chlorophyll-a, nitrogen and phosphorus in an eutrophic closed water. The model was characterized by 5 water quality indices of phytoplankton, organic matter, phosphate- phosphorus, dissolved inorganic nitrogen and dissolved oxygen (DO), and was applied to dynamic analysis of an agricultural pond in Fukuoka Prefecture, Japan, where concentrations of total nitrogen and total phosphorous were extraordinarily high. A comparison between calculations and observations showed that the ecosystem model developed could approximately reproduce the actual temporal fluctuation of chlorophyll-a, nitrogen, phosphorus and DO. The scenario analyses indicated that the 90% reduction of the current nutrient inflow load resulted in the remarkable decrease of total nitrogen and total phosphorous concentrations, fulfilling the water quality standard of paddy irrigation water in Japan.