Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and abundant in various media. Understanding the environmental behavior of PAHs in different compartments is essential for better evaluating and mitigating PAHs in the urban environment. Based on a 20-year monitoring dataset of PAHs in suspended particulate matter (SPM), this study investigates the variation, transport, and fate of PAHs in the Elbe River basin, and further projects the multi-interface transport of PAHs in the future. The results showed that the mean concentration of PAHs reduced from 6572.8 to 3388.2 ng g⁻¹ between 1998 and 2017 at the rate of −3.26%/year. However, the PAH pollution in the upper reach of the Elbe River was more serious than that in the middle and lower reaches, which implies a higher exposure risk in the upper reach. Self-organization mapping (SOM) and a positive matrix factorization (PMF) model identified vehicular emissions, which accounted for 44–81% of the total PAHs, as the predominant source of PAHs in the study area. According to a level III fugacity model, the impervious surface had the highest PAHs concentration (9.70 × 10⁻³ g m⁻³) and was identified as the main pathway of PAHs to receiving waters due to surface runoff. Furthermore, projection analysis indicated that the concentrations of PAHs in the various multimedia of the study area will be one order of magnitude lower in 2030 as a result of lower emission factors and the substitution of traditional fuels for vehicles with cleaner energies.