Abstract The coastal area adjacent to the Changjiang River estuary is a high‐risk region for harmful algal blooms. Both Changjiang River discharge and Kuroshio intrusion influence the hydrological conditions and nutrient composition in this area which could affect the onset of diatom and dinoflagellate blooms. However, current understandings on their roles in regulating different microalgal blooms are limited. In this study, changes in stratification, water masses, and the ratio of phosphorus to nitrogen were examined during the diatom and dinoflagellate blooms in 2005 using ship cruise data. The observations showed that both the diatom and dinoflagellate blooms occurred in the continental coastal water. By enhancing the pycnocline and phosphorus stress, the Changjiang diluted water plays an important role in affecting the diatom bloom. The dinoflagellate bloom is partly supported by the supply of phosphate transported by Kuroshio intrusion and upwelling. The results of this study will help elucidate the mechanisms of large‐scale harmful algal blooms in the coastal area adjacent to the Changjiang River estuary.