Current rates of urban development will result in water runoff becoming a major complication of urban water pollution. To address the worsening situation regarding water resource shortage and pollution, novel multilayer infiltration systems were designed and their effectiveness for removing pollutants in urban runoff tested experimentally. The multilayer infiltration systems effectively removed most pollutants, including organic matter (chemical oxygen demand (CODCr)), total nitrogen (TN), ammonia-nitrogen (NH4+-N) and total phosphorus (TP). CODCr, TN, NH4+-N, and TP were reduced by 68.67, 23.98, 82.66 and 92.11%, respectively. The main mechanism for nitrogen removal was biological nitrogen removal through nitrification and denitrification. Phosphorus in the urban runoff was removed mainly by fixation processes in the soil, such as adsorption and chemical precipitation. The results indicate that the proposed novel system has potential for removal of pollutants from urban runoff and subsequent reuse of the treated water.