Abstract: Based on data of heavy metal elements (Cu, Cr, Pb, Zn and Cd) in surface sediments recovered from Yangtze River Estuary and adjacent area in June, 2003 and April, 2007, the pollution and potential ecological risk degree have been assessed using three methods, namely, criterion of sediments quality standard, biological effect database-based approach and potential ecological risk indices. The results tell that concentration of Cu in the second-class sediments becomes increased after the first-stage water storage of the Three Gorges Project, occasionally producing negative biological effect, and Cr shows the opposite features. However,proportions of Pb, Zn and Cd in different sediment quality standards are relatively steady, with nearly no negative biological effect. In general, pollution extent and potential ecological risk were low in the study area. The pollution extent of typical pollutants is in the order of Cr > Cu > Zn > Pb > Cd and the potential ecological risk level of these heavy metals is showed as Cd > Cu > Cr > Pb > Zn. Moreover, Cd and Cu were main factors of potential ecological risks in the research area. Compared to that before the first-stage water storage, potential ecological risk index and risk level of heavy metals increased slightly in the early first-stage storage of the Three Gorges Project (2003), but the risk level in 2007 was similar to that during 1988-1992.