Hongze Lake is the first natural sink for transferring drinking water along the east route of the South-to-North Water Diversion Project in China. Thus, the assessment of health risk associated with sediment and soil in Hongze Lake is of vital importance in terms of protecting public health. This study surveyed the distribution of sixteen polycyclic aromatic hydrocarbons in different types of bank soils and sediments at the estuary area of Hongze Lake. The total concentrations of PAHs range between 562.4 and 1585.8 ng/g, and 3- and 4-ring PAHs are the majority in all samples, accounting for 78.2% to 92.3% of the total PAHs. Source analysis was conducted, and the results showed that PAHs in the estuary area mainly come from the burning of fossil fuels, leakage of oil products, low temperature combustion, biomass fuel, and transportation. The risk assessment of the study area showed that the K values of all the points were between 0.1~3, indicating that there was a low ecological risk. This study indicates that further policies for controlling pollution sources of PAHs are needed for reducing health risks associated with fresh water in Hongze Lake.