The ecological pattern, distribution and diversity of species of zooplankton in Changjiang Estuary and Hangzhou Bay were investigated and analyzed.On this basis, the impact of pollution on the zooplankton was discussed. It was discoveredthat the hemi-saline estuarine species, low salinity neretic species and temperate offshorespecies were dominating zooplanktons in the investigated areas. In accordance with thecomposition and morphology of the zooplanktons, it is still uncertain whether or notthe extent of the pollutants affected the species. However, the biomass of zooplanktonconsiderably decreased and a large amount of copper and zinc was accumlated in theplanktonic crustacean. Moreover, there occurred two times of red tide which wererespectively more than 30km² and 10 km² during the period of investigation. There-fore we should pay more attention to all these phenomena.