Estuarine plankton communities can serve as indicators of ecosystem modification in response to anthropogenic influences. The main objectives of this study were to describe the spatial distribution and diurnal variability in zooplankton abundance and biomass over almost entire salinity gradient of the Changjiang (Yangtze) River estuary and to provide a background reference for future studies. To accomplish this, data were collected from 29 stations in the estuary from May 19 to 26, 2003, including two anchor stations. The spatial and diurnal variations in zooplankton characteristics, i.e. abundance, biomass, and gross taxonomic composition, were examined. Generally, both the abundance and biomass gradually increased seaward and presented distinct spatial variations. In addition, the spatial data revealed a significant correlation between abundance and biomass; however, there was no significant correlation between abundance and biomass for the diurnal data. Although the zooplankton composition indicated distinct spatial differences in terms of dominant groups, copepods accounted for >50% of the total zooplankton abundance in most regions and times. Three zooplankton assemblages were recognized through hierarchical cluster analysis. These assemblages existed along the salinity gradient from fresh water to seawater, and their positions coincided with those of the three principal water masses in the estuary. The assemblages were classified as: (1) true estuarine, (2) estuarine and marine, and (3) euryhaline marine, which were characterized by the copepods Sinocalanus dorrii, Labidocera euchaeta, and Calanus sinicus, respectively. Both spatial and diurnal data indicated that there was no significant correlation between zooplankton abundance/biomass and depth-integrated phytoplankton abundance.