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In this study, an integrated ecological system was constructed to treat small scattered aquaculture wastewater in southern rural areas of China. The water outlet of 4 level wetlands was continuously monitored from July to December in 2017. Results showed the average concentrations of total nitrogen (TN), ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3-N), total phosphorus (TP) and chemical oxygen demand (COD) were 43.64mg/L, 17.53mg/L, 1.71mg/L, 1.66mg/L and 51.39mg/L in the average effluent concentration of grade I wetland, respectively, and 8.35mg/L, 4.42mg/L, 0.24mg/L, 0.26mg/L, 21.32mg/L in the average effluent concentration of grade IV wetland, respectively. The removal rates were 81%, 75%, 86%, 85% and 59% for TN, NH4+-N, NO3-N, TP and COD in the integrated ecological system, respectively. The effluents from the integrated ecological system met the requirements of “Discharge Standard of Pollutants for Livestock and Poultry Breeding” (GB 18596-2001) and achieved “Discharge Standard of Pollutants for Municipal Wastewater Treatment Plant” (GB 18918-2002) the center two levels to discharge the standard. Obviously, the integrated ecological system could work efficiently in treating the rural scattered aquaculture wastewater, and also possess merits of low construction and operation costs and simple management method, which will be benefited to its application in the southern rural regions of China.