In the present study, 28 polycyclic aromatic hydrocarbons (PAHs) were investigated in four sediment cores collected from the main river estuaries of Chaohu Lake, one of the severely polluted lakes in China. The results indicate that elevated concentrations of total PAHs (Σ28PAH) were found in the samples from the estuary of Nanfei River (ENF), considering BaP-based total toxicity equivalent (TEQ-BaP) and toxic unit (TU) results; there are potential adverse environmental implications. The total organic carbon (TOC) played an important role on the accumulation of PAHs at ENF and the estuary of Tongyang River (ETY). The predominant PAHs are high molecular weight (HMW) homologous for all samples; as a result, industrial wastewater from a steel company is expectedly the key source of PAHs in ENF, while coke consumption would be the important source of PAHs at other three sampling sites. Vertical distribution of PAHs in the sediment cores could be explained by the local social and economic activities. Furthermore, a minor variation of PAH composition in the sediment core could be justified by the stable structure of energy consumption in the Anhui Province. These results justify the need for further enhancement of industrial wastewater treatment and development of renewable energies which are the key factors on the control of PAH pollution in China.