River plumes represent a critical land-ocean continuum, yet studies on the dynamic changes of phytoplankton communities within these systems remain limited. Based on field measurements and remote sensing data, our research revealed the long-term dynamics of phytoplankton biomass, community structure distribution patterns, and their driving factors in the northern South China Sea and Taiwan Strait. The findings showed that nutrient limitation shifts and grazing pressure by microzooplankton, driven by the transport of the Pearl River plume, resulted in changes to the phytoplankton community structure. Additionally, the coupling of coastal upwelling and plume interactions, influenced by wind forces, was identified as a significant factor affecting phytoplankton dynamics. These insights shed light on the complex interactions governing phytoplankton dynamics and contribute to a broader understanding of ecosystem functioning in marine environments influenced by river plumes.