Storm-induced overflows make stormwater drainage systems critical pathways for transporting emerging contaminants, such as heterocyclic polycyclic aromatic hydrocarbons (HPAHs), to surface waters, particularly during storms. HPAHs exhibit greater mobility, bioavailability, toxicity, and odor potential than conventional PAHs, however, uncertainties regarding their source apportionment and environmental fate hinder targeted mitigation. Utilizing a Chemical Mass Balance model, we quantified HPAH sources in stormwater overflows and determined that sewer sediments contributed 34%-62% of total HPAH concentrations and 46.7%-51.5% of risk quotient, thereby identifying sewer sediment as primary source. Further stormwater disturbance simulations revealed that low-molecular-weight HPAHs preferentially accumulate on particles, while high-molecular-weight dibenzofuran (DBF) and dibenzothiophene (DBT) readily desorb into water with resuspended sediments. Combined predictions from Ecological Quantitative Structure-Activity Relationship models and desorption experiments revealed that DBF and DBT's higher ecotoxicity and elevated release efficiencies synergistically challenge end-of-pipe removal, potentially posing long-term aquatic risks. Density Functional Theory analyses further clarified that large LUMO-HOMO energy gaps and neutral surface electrostatic potentials of DBF and DBT collectively diminish their adsorption affinity to sediment particles. By quantifying sewer sediment contributions and elucidating the specific transport mechanisms of HPAHs, this study provides a scientific foundation for the management of emerging contaminants in stormwater systems.