Abstract: A multi-stage filtration system was built to indicate the impact of the loading rate on its performance in removing pollutants in agricultural runoff, which was located next to Lushan river in Gaofeng Town of Chongqing . The system was adaptive to variation of inflow quality and quantity. The average removal rates of chemical oxygen demand (COD), ammonia (NH4+-N), total nitrogen (TN) and total phosphorus (TP) were 35%, 73%, 37% and 54%, respectively. The effluent concentration increased with the increase of influent loading linearly. There was a significant logarithmic correlation between removal loading per unit area of the system and influent loading. The system was stable at low influent loading, but at high influent loading, the removal rate varied more. The removal loading and the effluent loading decreased steadily with the increase of the stages. Characteristics of clarification, vegetative filter strips and biological contact oxidation pond were combined in the filtration system.