With the rapid development of urbanization, heavy metal pollution resulting from runoff has increased and also varies significantly according to different land uses. Research is still lacking, however, on the risk assessment of heavy metals carried by the runoff. In the Wuhu urban area, we selected seven types of land use, i.e., road square land, green land, commercial land, residential land, industrial land, public building land, and dock land, to monitor the content of copper (Cu), cadmium (Cd), and lead (Pb) in rainfall runoff. Furthermore, we evaluated the ecological risk of these three heavy metals by risk quotient (RQ), which was developed on the basis of the predicted no-effect concentration (PNEC) obtained by the species sensitivity distribution (SSD) curve. According to the event mean concentration (EMC) of four effective rainfall events, compared with the Environmental Quality Standard for Surface Water (GB 3838–2002), the statistical results showed that Cu, Cd, and Pb in the rainfall runoff met Class II, IV, and V water quality standards, respectively, which were affected mainly by the traffic activities and roofing materials in different types of land use. Industrial land has experienced the worst pollution from all three of these heavy metals, and the other areas have been polluted to different degrees by different heavy metals, which has resulted in significant differences in toxicity to aquatic organisms. Generally, the ecological risks posed by heavy metals in rainfall runoff have a high-risk degree, in the order of Cd < Pb < Cu. The ecological risk of Cu and Pb to freshwater organisms is high, and that of Cd is medium. Therefore, the current environmental quality standard for surface water in some areas like Wuhu City, China, has not fully considered the ecological impact and has underestimated the ecological risks of heavy metals.