The rapid expansion of urban impervious surface areas complicates urban-scale heavy metal circulation among various environmental compartments (air, soil, sediment, water, and road dust). Herein, a level III steady-state aquivalence model evaluated the fate of heavy metals in Nanjing, China. Iron was the most abundant heavy metal in all environmental compartments, while cadmium was the rarest. Most simulated concentrations agreed with measured values within three logarithmic residuals. In the simulated heavy metal cycle, industrial emission contributed almost the entire input, whereas sediment burial was the dominant output pathway. The transfer fluxes between bottom sediment and water were the highest. Thereinto, the contribution of sediment resuspension for Fe and Mn was significantly higher than that to the other metal elements, which could partly explain why Fe and Mn are the major blackening ingredients in malodorous black rivers. Road dust was also an important migration destination for heavy metals, accounting for 3–45%, although soil and sediment were the main repositories of heavy metals in the urban environment. The impact of road dust on surface water should not be neglected, with its contribution reaching 4–31%. The wash-off rate constant W for road dust–water process was proved to be consistent with that for film–water and was independent of the type of heavy metals. Sensitivity analysis highlighted the notable background value effect on Fe and Mn.