Abstract: We measured 7 heavy metals (Cr, Co, Ni, Cu, Zn, Cd and Pb) in surface sediments of Anhai Bay and Weitou Bay in April 2017. The results showed that the average concentration of Cr, Co, Ni, Cu, Zn, Cd and Pb are 96.99，13.35，33.53，39.68，132.87，0.17 and 39.10 μg/g, respectively. The distributions of heavy metals showed a decreasing tendency from the northwest to the southeast, with a slight increment near the shore in the southeast areas we studied. It is suggested that it is from the input of terrestrial sources. However, the trend is not so obvious for the Co distribution. The concentrations of Cd and Pb in all of the sampled stations were classified as the first grade by national standard Marine Sediment Quality. At 35%, 71% and 71% of the studied stations the concentrations of Cr, Cu and Zn were met the first grade by the Marine Sediment Quality. Thus, the remaining stations only met the second or the third grade. We used principal component analyze to analysis the source of heavy metals in Anhai Bay and Weitou Bay. The results showed that the sources of Cr, Cu, Zn, Cd and Pb were associated with the anthropogenic sewage input. The source of Ni was mostly from the weathering during the geochemical process besides the anthropogenic input while the source of Co is mainly due to the weathering in the bays. The potential ecological risk index is used to evaluate the contamination degree of heavy metals and the potential influence in Anhai Bay and Weitou Bay. The result showed there was a strong ecological risk in the studied area where the measures should be taken to control the sources of heavy metal pollution and to strengthen the environmental protection.