Methods of indexes of geo-accumulation, potential ecological risk index,and biological effects of concentration are applied to evaluate the eco-environmental quality of sediments in the Changjiang estuary and its adjacent waters which are divided into 7 zones by Cluster analysis in consideration of hydrodynamic process and deposition process and salinity impact. The results showed that three methods of evaluation findings are basically the same, The environment of the foundation of the study area is subject to varying degrees of heavy metal pollution, while the quality of sediments outside of the estuary and sea area nearby Zhousan is good and poor at the estuary and turbidity maximum Zone and Hangzhou bay. The degree of Hg spatial fluctuation appears to be the highest in surface sediments, with the order of heavy metals fluctuation degree ranging as the following：Hg>Cd>Cu>Pb>As>Zn. Ecological responses are obviously discovered in the validation based on the corresponding period macrobenthic community parameters.