An eco-restoration system to remove excess nutrients and restore the agricultural ecosystem balance was proposed and applied from August 2006 to August 2008 in a residential-cropland complex area (1.4Â Ã—Â 105Â m2) in Kunming, western China, where the self-purifying capacity of the agricultural ecosystem had been lost. The proposed eco-restoration system examined includes three main foci: farming management, bioremediation, and wastewater treatment. The results showed that the removal efficiencies of total phosphorus (TP) and total nitrogen (TN) from the complex wastewater were 83% and 88%, respectively. The Simpson's diversity indices of macrophytes and zoobenthos indicated that the system had increased macrophyte and zoobenthic diversity as well as improved growth conditions of the plankton habitats. The results demonstrated that the proposed eco-restoration system is a promising approach for decreasing the output of nutrients from soil, improving agricultural ecosystem health, and minimizing the downstream eutrophication risk for surface waters.