The contents of 16 priority water-borne polycyclic aromatic hydrocarbons (PAHs) in water, potential external pollution sources and sediment from the famous landscape of the Qinghuai River were measured by gas chromatography—mass spectrometry (GC-MS). The distribution, composition, source and ecological risk of PAHs were analyzed. The following results were obtained: (1) Benzo[a]pyrene and benzo[ghi] perylene were not detected in all samples. The total contents of 16 priority PAHs (PAH16) varied from 52.5 to 745.3 ng l−1 with the average of 174.0 ng l−1 in water, from 96.0 to 1,064.6 ng l−1 with the average of 329.2 ng l−1 in potential sources, from 931.7 to 15,295.5 ng g−1 with the average of 7,133.6 ng g−1 in sediments. (2) The concentration of PAH16 in water is lower than in sediment and higher rings are more easily detected in sediment. The percentage of higher ring (four- to six-rings) PAHs accounted for more than 55.6% of PAHs in sediment. (3) The value of FLA/(FLA+Pyr) was higher than 0.5 at most sampling points which illustrated the source was related with petrogenic such as liquid fossil fuel combustion. (4) The potential ecosystem risk of low ring PAH for upstream conflux of external Qinhuai River was less than 10%, while it was 10–50% for other sampling points; The four rings PAH shows lower potential ecosystem risk than other ring PAH in this study area; Dibenzo [ah] anthracene (DahA) shows high potential ecosystem risk at all sampling points.

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