The purpose of this paper is to analyze nutrients dynamics depending on biomass of Menyanthes trifoliata L., the endangered species, in a small closed-type wetland. In order to understand dynamics between Menyanthes trifoliata L. and eutrophication, causal loops and stock-flow diagram were constructed. The result of the model simulation was matched well with monitoring data (Menyanthes trifoliata L. biomass, TN, TP, DO). The model was simulated with 3 scenarios. In case of scenario 1, the initial value of biomass was 0mg/L, and the eutrophic state period was 77 days. In case of scenario 2, the initial value of biomass was 35.8 mg/L, and the eutrophic state lasted for 13 days. In case of scenario 3, the initial value of biomass was 71.6 mg/L, and the eutrophic state was nonexistent. The scenario 3 was selected as planting plan of Menyanthes trifoliata L. Through this study, planting design with an endangered plant was developed to control eutrophication in small closed-type wetland.