A multimedia fugacity model with spatially resolved environmental phases at an urban scale was developed. In this model, the key parameter, organic matter, was replaced with black carbon (BC) and applied to simulate the distributions of phenanthrene (Phe), pyrene (Pyr) and benzo[α]pyrene (BaP) in Nanjing, China. Based on the estimated emissions and measured inflows of air and water, the Phe, Pyr and BaP concentrations in different environment media were calculated under steady-state assumptions. The original model (OC-Model), BC-inclusive model (dual C-Model) and improved model (BC-Model) were validated by comparing observed and predicted Phe, Pyr and BaP concentrations. Our results suggested that lighter polycyclic aromatic hydrocarbons (PAHs) were more affected by BC substitution than their heavier counterparts. We advocate the utilization of sorption with BC in future multimedia fate models for lighter PAHs based on the comparison of the calculated and observed values from measured and published sources. The spatial distributions of the Phe, Pyr and BaP concentrations in all phases were rationally mapped based on the calculated concentrations from the BC-Model, indicating that soil was the dominant sink of PAHs in terrestrial systems, while sediment was the dominant sink of PAHs in aquatic systems.