This study focuses on the analysis of the long-term trends and source apportionment of PAHs in the suspended sediments of the Elbe River in Saxony, Germany, from 2001 to 2016. The results of the Mann-Kendall trend test indicated that the concentrations of total and individual PAHs exhibited decreasing trends during the 16-year study period. According to the positive matrix factorization (PMF) receptor model, primary sources for every four-year period were identified as oil burning, biomass burning, and vehicular emissions from gasoline and diesel-powered engines. The changes in the sources were consistent with the trends in vehicle numbers and energy consumption during the last 16 years. Furthermore, the results of total toxic benzo[a]pyrene equivalent (TEQ) values indicated potential cancer risks. The results of the mean hazard quotient (MHQ) suggested that PAHs exhibited a 21% probability of being toxic to benthic organisms and to the aquatic environment.