This study utilized the ecological engineering measures to treat the 'heavy-polluted' river which was contaminated by rural wastewater using 'river pollution index' The water quality indice, water body classification, 'water quality indicator' (WQI) including NSF-WQI, WQI5 and WQI8 and RPI were used to evaluate the design function. After 18 months monitoring, the system performance was improved to the condition of 'medium-polluted' level in terms of RPI. The effluent reached to D category based on surface water body classifications and water quality standards. The results indicate that WQI5 is a sensible and practical index. Hence, this study demonstrates that the water quality monitoring combined with WQI5 evaluation can be an important and convenient method. Meanwhile, the proposed system is also feasible.