The aim of this project was to establish an economical and environmentally benign biotechnology for removing nutrients from non-point source wastewater. The proposal involves a hybrid bioreactor comprised of sequential anaerobic, anoxic and aerobic (A2/O) processes and an eco-ditch being constructed and applied in a suburban area, Kunming, south-western China, where wastewater was discharged from an industrial park and suburban communities. The results show that the hybrid bioreactor fosters heterotrophic and autotrophic microorganisms. When the hydraulic load is 200 m3 per day with the running mode in 12-hourly cycles, the removal efficiencies of the nutrients were 81% for TP, 74% for TDP, 82% for TN, 79% for NO3-N and 86% for NH4-N. The improved bacterial community structure and bacterial habitats further implied enhanced water quality and indicates that the easily-deployed, affordable and environmentally-friendly hybrid bioreactor is a promising bio-measure for removing high loadings of nutrients from non-point source wastewater.