Two long sediment cores were sampled at the Quanzhou Bay, southeast China, and ten heavy metal (Cr, Cu, Zn, Cd, Pb, Co, Ni, Fe, Mn, and Hg) concentrations and Pb isotope compositions were measured in order to evaluate background values, assess contamination levels, and identify pollution sources. The regional background levels of heavy metals in Quanzhou Bay are established using the fine-grained samples (< 63 μm) obtained from the deep non-contaminated core sediments. The background values (ranges) of the elements Cr, Cu, Zn, Cd, Pb, Co, Ni, Mn, Hg, and Fe are 37.14 (25.96-48.33), 19.79 (12.51-127.00), 130.86 (96.47-165.26), 0.24 (0.18-0.29), 42.18 (37.40-46.96), 10.31 (9.55-11.08), 20.89 (19.82-24.54), 612.6 (524.46-923.54) , 0.070 (0.06-0.09) mg kg-1 and 3.17 (2.96-3.83) %, respectively. The background values of most elements proposed for Quanzhou Bay in this study are in the middle range of those proposed for other sites in China. However, the Pb and Zn background values are significantly higher than the average of China. Due to their relative higher enrichment factor (EF), geo-accumulation indexes (Igeo), and contamination factor (CF) of Cu, Zn, Pb, Mn, and Cd in the sediments at 10-140 cm depths, these heavy metals are suggested to have a long contamination history since nineteenth century. Based on the principal component analysis (PCA) and cluster analysis (CA), Cu, Zn, and Pb are clustered to a group and their sources are possible to be related with the mining of the metallic ore deposits. The result of Pb isotope composition in the core sediments further indicates that the source of Pb transferred from the natural source at early period to the lead-zinc ore during 1788-1921 AD, then changed to the integrated anthropogenic sources, including Pb-Zn ore deposits, industrial and domestic emissions in recent decades. In conclusion, our results may help to construct the specific measures for the environment management in Quanzhou Bay and its river inputs.