The Changjiang Estuary and adjacent sea area in the East China Sea suffer from frequent harmful algal blooms. However, the relative importance of riverine nutrient input from the Changjiang River and oceanic nutrient input from the Taiwan Warm Current and Kuroshio Current to the development and distribution of summer phytoplankton blooms in this area remains unclear. To address this problem, we deployed a coupled physical-biological model. The coupled model successfully reproduces the main hydrographic and biogeochemical features in this domain. Both satellite observations and model results show two regions of elevated chlorophyll concentrated in this site. Simulated results show that harmful algal blooms in the region north of the Zhoushan Islands are mainly driven by riverine nutrients from the Changjiang River, while algal blooms in the region south of the Zhoushan Islands are mainly controlled by nutrients from the open ocean. Nutrient input, particularly phosphate, from the Kuroshio subsurface water contributes most to the accumulation of dinoflagellate biomass and chlorophyll in the southern region, while the Taiwan Warm Current has less influence. This has implications for nutrient control and land management practices: Although reducing riverine nutrient loads may significantly reduce phytoplankton growth north of the Zhoushan Islands, it will have little effect in the area to the south. Plain Language Summary Blooms of microscopic algae that can be harmful to marine ecosystems and commercial fisheries are increasingly common during the summer months in the Changjiang Estuary and adjacent sea area in the East China Sea. The Changjiang River is traditionally considered as the dominant source of nutrients driving these harmful algal blooms. In this study, we show that although this appears to be true for algal blooms occurring to the north and northeast of the river estuary, algal blooms that occur along the coast to the south of the river estuary are mainly regulated by nutrient input from the open ocean. Intrusion of the Kuroshio subsurface water to the south of the Changjiang Estuary is shown to be particularly important in supplying the dissolved phosphate necessary for the algae in the southern region to bloom in large quantities.