Abstract: Based on the survey data of surface sediment in the Yangtze River Estuary and Hangzhou Bay in May (spring) and August (summer) from the year 2003 to 2019, this study analyzed the time series of heavy metals including Cu, Zn, Pb, Cd, Hg and As in the surface sediment. The purpose of this study was to understand the changing trends and the main influencing factors of heavy metals at a long temporal scale. The potential harm of six metals were studied by the method of Hakanson’s ecological risk assessment. The results showed that the contents of Cu, Zn, Cd, Hg and As in the surface sediments of the Yangtze River Estuary and Hangzhou Bay showed an overall decreasing trend with the years, while the content of Pb showed no obvious change trend but fluctuated greatly. The potential ecological risks of six heavy metals were listed as Cd>Hg>As>Cu>Pb>Zn, in which Cd and Hg were the major potential ecological risk contributors. The comprehensive potential ecological risk index of the six heavy metals decreased significantly with the year, and the comprehensive potential ecological risk of the six heavy metals decreased to slight ecological risk after 2010.