A flood irrigation system was constructed to remove nutrient-based water pollutants through the various natural treatment mechanisms of plants and microorganisms. Species of plants were allowed to proliferate naturally within the system. The succession of flora was then utilized as an index to evaluate the water purification efficiency of the flood irrigation system. The natural growth of plants during the test period indicated what part of the irrigation system would recover most efficiently from nutrient-based contamination. From the first stage of observation (50 days) to the second stage (50 days), the average processing efficiencies of Nitrate Nitrogen (NO3 −-N) and Ortho-phosphate (PO4 3−) were improved 1.7% and 70.3%, respectively. After the 60th day, the Compositae family flourished in the system. At the same time, removal rate of Nitrate Nitrogen was increased dramatically which may be related to prevalence of the Compositae family. Trends indicate that the Ortho-phosphate concentration of the irrigated water was low, and Brachiaria mutica of Poaceae were dominant which may have lead to the phenomenon of phosphorus released in the flood irrigation system.