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This study aimed to gain a clear understanding on the status of pollution by heavy metals in the petrochemical sewage and the potential ecological risk caused by heavy metal pollution in the sea area of Daya Bay. The contents and spatial distributions of heavy metals including Zn, Pb, Cu, Cd, Cr, As and Hg in seawater, sediment and fishes collected from Daya Bay were analyzed. The comprehensive pollution index (CPI) and ecological risk indexes (ERIs) were used to evaluate the contaminated severity and potential ecological risks of heavy metals in seawater and sediment. The results showed that the contents of these heavy metals, except for those of Zn and Pb, in several stations set in Daya Bay from 2011 to 2012 were relatively low, which were lower than the quality standard of class I according to the China National Standard Criteria for Seawater Quality, suggesting that the seawater in Daya Bay has not been polluted yet by these heavy metals. The average CPI of heavy metals in seawater during flooding season (0.72) was higher than that during dry season (0.38) whereas the average CPI of heavy metals in sediment during dry season (7.77) was higher than that during flooding season (5.70). Hg was found to be the primary contaminating heavy metal in sediment during dry season, which was followed by As and Zn whereas during flooding season, Hg was the primary contaminating metal in sediment, followed by Zn and Cu. The contents of these 7 heavy metals in fishes collected from the surveyed areas were lower than those of the standard requirements. A correlation analysis indicated that there were significant differences in the correlations between the midst of the heavy metals in sea water and the different periods. The ERIs of heavy metals in sediment during dry season (129.20) was higher than that during flooding season (102.86), and 25% of the sampling sites among all stations were under the risk of high-level alarm. The potential ERIs of heavy metals in sediment in offshore waters were higher than those of inshore waters, and were higher in the bay-mouth than in the bay-head. However, the distributions of potential ERIs showed reversed trend during dry season. The comprehensive assessment results showed that Hg was the primary heavy metal with a high ecological risk whereas the potential ERIs for the other six heavy metals in the petrochemical sewage waters in Daya Bay were relatively low.