A three-stage filtration system, which locates next to Lushan River in Gaofeng Town of Chongqing, is built to make clear its effects on controlling the runoff pollution. The system is adaptive to variation of inflow quality and quantity. The average removal rates of SS, NH+4-N, TN and TP are 80%, 78%, 37% and 48%, respectively. The concentrations of various pollutants decrease gradually along the way with the increase of filtration system stages. The removal rates of TN and NH+4-N increase steadily with the increase of stages, but SS and TP don’t. In the system, the removed nitrogen during the first stage is mainly in particulate state and in dissolved state during the second and third stage. The removal rate of particulate phosphorus in the first and second stage is better than in the last one. In the third stage, the removals of particulate phosphorus and dissolved phosphorus are almost the same. In the first stage, the removal rates of various pollutants are at the highest level, and the nitrification is strong. Compared with the first stage, the removal efficiency of NH+4-N and TN in the second stage is relatively high. The removals of NH+4-N, TN and TP are low in the last stage, while the removal rate of SS is almost same to the second.