Marine phytoplankton are vital for global primary production and carbon fixation in marine ecosystems. Understanding the distribution patterns and assembly mechanisms of phytoplankton in varying nutrient conditions is crucial for phytoplankton ecology, yet research in this field is limited. This study employed environmental DNA technology targeting the phytoplankton 23S rRNA gene to investigate the community structure and assembly processes of phytoplankton (algae and cyanobacteria) in the East China Sea. We identified 224 phytoplankton species: 72 Bacillariophyta, 44 Cyanobacteria, and 34 Chlorophyta. Bacillariophyta and Dinoflagellata were predominant in the nutrient-rich Changjiang Diluted Water (CDW), while cyanobacteria dominated in the low-nutrient Kuroshio Branch Current (KBC). Phytoplankton distribution was significantly influenced by salinity and nutrient levels. Deterministic processes mainly governed phytoplankton community assembly in both CDW and KBC. Co-occurrence network analysis revealed that interactions among phytoplankton in the KBC were significantly higher than in the CDW, indicating greater cooperation or competition in the KBC. Conversely, the modularity of the CDW network was notably higher, likely due to greater environmental heterogeneity. This study highlights the effectiveness of environmental DNA technology in exploring phytoplankton community structure and assembly mechanisms in different nutrient environments. These findings emphasize the significance of understanding phytoplankton dynamics, as enhanced carbon fixation could greatly impact carbon cycling and climate regulation in marine ecosystems.