Abstract: Recent researches of PAHs in sediment mainly were focused on offshore areas of Yangtze River estuary and coastal areas nearby Shanghai. However, there were few reports about the PAHs in waterway sediment from Qidong and Chongming Island. Surface waterway sediment samples (0-20 cm) were collected from Qidong and Chongming Island. Followed by extraction using accelerated solvent extraction techniques, then 14 PAHs were measured by means of HPLC-FLD in order to discuss and assess the distribution characteristics, possible sources and ecological risks of PAHs, respectively. The results showed that 14 PAHs could be detected in varying degrees for all sampling sites, Total concentrations of PAHs ranged from 83.43 to 5206.97ng/g with a mean concentration of 736.95 ng/g. 2, 3, 4-ring PAHs dominated in waterway sediment samples, and phenanthrene was the most abundant individual compound, accounting for 9.04% to 24.06% of total concentrations of PAHs, followed by fluoranthene and pyrene. The percentage of benzoapyrene with high carcinogenicity in all samples was from 0.94% to 10.68%. Compared with other similar regions of the world, PAHs in waterway sediments from Qidong and Chongming Island of Yangtze River estuary were at moderate level. The sources of PAHs were apportioned using ratio analysis. Places with Phe(phenanthrene)/Ant(anthracene) < 10 and Fla(fluoranthene)/Pyr(pyrene)≥1 accounted for 56.25% of all sampling sites, indicated that PAHs in the studying areas mainly derived from combustion of fuel oil. Oil spill was another important source for some sampling sites located nearby harbours and wharfs. Some sites presented combined pollution characteristics. Comparing with ERL and ERM values for environment risk evaluation, some sampling sites of this area possessed a potential combined ecological risk to local organisms caused by PAHs.