In this study, concentrations, distribution between different phases, transition along the Middle and Lower reaches of the Yellow River and possible sources of PAHs were assessed. Results demonstrated that the relative proportions of 15 PAHs in all stations of the main River were similar, with concentrations of benzo[a]pyrene all above drinking water standards in most of the stations sampled. PAHs concentrations in tributaries were higher than those in the corresponding sites in the main River. PAHs concentrations of suspended particles were mainly correlated with contents of total organic carbon. However, PAHs concentrations in sediments were mainly correlated to the volume of particles with size smaller than 0.01 mm. The distribution of PAHs in all media sampled indicated that sediments could act as a sink/source for PAHs in different sections and source analysis revealed that PAHs mainly originated from coal burning, although in some tributaries PAH inputs could come from combustion of petroleum.