The urban lakes in China, especially those with relatively small areas and closed watersheds, have suffered from serious pollution and are at a high risk of eutrophication due to the small amount of concern given to them. The temporal distribution profile, source apportionment and potential toxicity of parent polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs (APAHs) in a sediment core from an urban shallow lake with the above specifications, in the middle and lower reaches of the Yangtze River, China, were investigated in the present study. Parent PAHs, especially 4-6 ring ones, were dominant in the sediment core. The vertical profiles of 16 anthropogenic US Environmental Protection Agency (EPA) priority PAHs increased from a depth of 50 cm to 30 cm, then slightly decreased to the surface. However, biogenic perylene content decreased from bottom to surface. Most of the APAHs increased in concentration from bottom to surface. Source apportionment of EPA PAHs indicated the pyrogenic source was dominant in the sediment core. The domestic combustion of bituminous coal, coal tar and biomass can be identified as the main factors responsible for this. Toxicity assessment of selected parent PAHs demonstrated that benzo(a)pyrene accounted for the largest part of the toxic equivalent quantity (TEQ), and PAHs in the studied area possibly imposed adverse biological effects, especially for benthic organisms. Therefore, action should be taken to prevent an increase in the contamination from PAHs in the studied area, as well as in similar urban lakes in China, based on the specificity of individual watersheds.