Polycyclic aromatic hydro-carbons (PAHs) are carcinogenic, mutagenic, and teratogenic persistent organic molecules. To protect human health and aquatic organisms, a systematic assessment of the trends in PAH exposure risk and the key emission sources governing such trends is essential. Therefore, the long-term trends in PAH concentrations were assessed for the Elbe River, Germany, which represents a dynamic environment in which anthropogenic activities and nature exhibit complicated interactions. A Mann-Kendall trend test identified a general decreasing trend (a 38% reduction) in PAH concentrations over the last 16 years (2001–2016), which was consistent with a decline in the relative contribution from coke oven use (a 26–14% reduction). According to the source apportionment, an increasing number of source contributors were identified over time. Furthermore, PAH exposure risks for aquatic organisms and human health were calculated as risk quotient (RQ) and chronic daily intake (CDI). For most PAHs, the risk quotient of negligible concentrations (RQNCs) exceeded 1 and the risk quotient of maximum permissible concentrations (RQMPCs) was less than 1, indicating a middle-level ecological risk. In addition, the CDI-based hazard quotients suggested that the risk of human exposure to PAHs remained within acceptable limits during the study period. However, vehicular-associated benzo(a)pyrene (BaP) emissions contributed the most to human health risk. The data presented here suggest that substituting petroleum and coal with green energies will reduce PAH concentrations in aquatic environments.