Polycyclic aromatic hydrocarbons (PAHs) have received extensive attention because of their widespread presence in various environmental media and their high environmental toxicity. Thus, figuring out the long-term variances of their occurrence and driving force in the environment is helpful for environmental pollution control. This study investigates the concentration levels, spatial variance, and source apportionment of PAHs in suspended particulate matter of Freiberger Mulde river, Germany. Results show that the concentrations of the 16 priority PAHs suggested by USEPA (Σ16PAHs) were in the range of 707.0–17,243.0 μg kg⁻¹ with a mean value of 5258.0 ± 2569.2 μg kg⁻¹ from 2002 to 2016. The relatively high average concentrations of Σ16PAHs were found in the midstream and upstream stations of the given river (7297.5 and 6096.9 μg kg⁻¹ in Halsbrucke and Hilbersdorf, respectively). In addition, the annual average concentration of Σ16PAHs showed an obvious decreasing pattern with time. Positive Matrix Factorization (PMF) receptor model identified three potential sources: coke ovens (7.6–23.0%), vehicle emissions (35.9–47.7%), and coal and wood combustion (34.5–47.3%). The source intensity variation and wavelet coherence analysis indicated that the use of clean energy played a key role in reducing PAHs pollution levels in suspended sediments. The risk assessment of ecosystem and human health suggested that the Σ16PAHs in the given area posed a non-negligible threat to aquatic organisms and humans. The data provided herein could assist the subsequent management of PAHs in the aquatic environment.