•Sedimentary PAHs in Guan River Estuary were investigated for the first time.•PAH concentrations were low in comparison with other estuaries around the world.•PAH concentrations appeared to be negatively correlated with sediment grain size.•Sedimentary PAHs in GRE mainly originated from pyrolytic sources.•Sedimentary PAHs in GRE indicated low negative effects except FLO. The contamination of surface sediments in Guan River Estuary, China, by polycyclic aromatic hydrocarbons (PAHs) has been fully investigated. Total concentrations of 21 PAHs ranged from 90 to 218ng/g with an average of 132.7ng/g, which is relatively low in comparison with other estuaries around the world. PAH concentrations appeared to be positively correlated with clay content and negatively correlated with sediment grain size. Source identification implied that the PAHs originated mainly from pyrolytic sources. However, source patterns may be continuously changed to a petrogenic origin due to the heavy ship traffic and continuous discharge of oily sewage in this area. The PAH levels were also compared with international Sediments Quality Guidelines and Sediments Quality Criteria, and the results indicated low negative effects for most individual PAHs. However, toxic effects related to FLO would occur occasionally in most locations in the estuary.