A comprehensive study on the phytoplankton standing stocks, species composition and dominant species in the eutrophic Changjiang(Yangtze River) Estuary(CE) was conducted to reveal the response of phytoplankton assemblage to Changjiang Diluted Water(CDW) and upwelling in the spring. Phytoplankton presented peak standing stocks(13.03 μg/L of chlorophyll a, 984.5×103 cells/L of phytoplankton abundance) along the surface isohaline of 25. Sixty-six species in 41 genera of Bacillariophyta and 33 species in 19 genera of Pyrrophyta were identified, as well as 5 species in Chlorophyta and Chrysophyta. Karenia mikimotoi was the most dominant species, followed by Prorocentrum dentatum, Paralia sulcata, Pseudo-nitzschia delicatissima and Skeletonema costatum. A bloom of K. mikimotoi was observed in the stratified stations, where the water was characterized by low nitrate, low phosphate, low turbidity, and specific ranges of temperature(18–22 °C) and salinity(27–32). K.mikimotoi and P. dentatum accumulated densely in the upper layers along the isohaline of 25. S. costatum was distributed in the west of the isohaline of 20. Benthonic P. sulcata presented high abundance near the bottom,while spread upward at upwelling stations. CDW resulted in overt gradients of salinity, turbidity and nutritional condition, determining the spatial distribution of phytoplankton species. The restricted upwelling resulted in the upward transport of P. sulcata and exclusion of S. costatum, K. mikimotoi and P. dentatum. The results suggested that CDW and upwelling were of importance in regulating the structure and distribution of phytoplankton assemblage in the CE and the East China Sea. A comprehensive study on the phytoplankton standing stocks, species composition and dominant species in the eutrophic Changjiang (Yangtze River) Estuary (CE) was conducted to reveal the response of phytoplankton assemblage to Changjiang Diluted Water (CDW) and upwelling in the spring. Phytoplankton presented Sixteen-six species in 41 genera of Bacillariophyta and 33 species in 19 genera of Pyrrophyta were identified, as well as 5 species in Chlorophyta and Chrysophyta. Karenia mikimotoi was the most dominant species, followed by Prorocentrum dentatum, Paralia sulcata, Pseudo-nitzschia delicatissima and Skeletonema costatum. A bloom of K. mikimotoi was observed in the stratified stations, where the water was characterized by low nitrate, low phosphate, low turbidity, and specific ranges of temperature (18-22 ° C) and salinity (27-32). K. mikimotoi and P. denta tum accumulated densely in the upper layers along the isohaline of 25. S. costatum was distributed in the west of the isohaline of 20. Benthonic P. sulcata presented high abundance near the bottom, while spread upward at upwelling stations. of salinity, turbidity and nutritional condition, determining the spatial distribution of phytoplankton species. The restricted upwelling resulted in the upward transport of P. sulcata and exclusion of S. costatum, K. mikimotoi and P. dentatum. The results suggested that CDW and upwelling were of importance in regulating the structure and distribution of phytoplankton assemblage in the CE and the East China Sea.