As an important water purification and seepage measure for sponge cities, biofiltration systems have been widely used in their construction in China. In order to identify the heavy metal accumulation, pollution, and its potential environmental risk in the biofiltration systems, this study examined the heavy metal contents and spatial distribution characteristics by taking the biofiltration systems of Yuelai new town, Chongqing, the first demonstration area of sponge city construction in China, as the research object, and conducted a risk evaluation of the pollution level and ecological environment in this new town using the contamination factor (CF), geo-accumulation Index (Igeo), and potential ecological risk coefficient (PERC). The results showed that, except for Mn, the average contents of Cu, Zn, Pb, Ni, and Cd in the biofiltration systems of Yuelai new town were 4.14, 1.77, 4.98, 1.23, and 6.51 times higher than the soil background values of Chongqing. In terms of spatial distribution, the contents of heavy metals in biofiltration systems along the roads in different functional areas showed great differences. The contents of Cu, Zn, Mn, Pb, Ni, and Cd in the industrial area were significantly higher than those of the same types of heavy metals in the biofiltration systems in other areas (P<0.05). The CF and Igeo showed that the pollution level of heavy metals was ranked as follows:Mn<Zn<Ni<Cu<Pb<Cd. Among them, Cu and Pb were highly polluted, Cd was severely polluted, and the PERC of Cd was 194.13, which indicated a high risk; the remaining heavy metals were at a minor risk. The pollution contribution of Cd to the composite PERC of all heavy metals was 78.73%, which was the major source of heavy metal potential risk. After the long-term operation of the biofiltration systems in a sponge city, certain environmental and ecological risks may exist later due to the accumulation of filler heavy metals. Hence, it is necessary to strengthen the operation management and carry out research on the non-polluted management of the filler of biofiltration facilities, to prevent them from becoming a new source of urban heavy metal pollution.