Phytoplankton communities are key components of coastal ecosystems and sensitive indicators of environmental gradients in estuary–bay continua. However, due to large spatial and seasonal variations driven by terrestrial inputs, estuarine mixing, and bay-interior exchange, the processes organizing phytoplankton biomass and community structure across adjacent estuarine and bay systems remain poorly understood. Here, we investigated phytoplankton biomass, major group composition and community–environment relationships in the Zhangjiang Estuary–Dongshan Bay continuum, a subtropical estuary–bay system in southern Fujian, by integrating 31 seasonal cruises from 2021 to 2025 with HPLC pigment measurements, CHEMTAX analysis and multivariate statistics. Results showed significant spatial variations in phytoplankton biomass and community composition along the continuum, with total chlorophyll a generally decreasing from the low-salinity estuarine end to the high-salinity bay end. This decrease was not simply linear, as relatively high biomass was maintained in the low- to lower-mesohaline section, around salinities of 10–15. The composition of major phytoplankton groups also changed markedly, with chlorophytes, cyanobacteria, cryptophytes, and diatoms jointly contributing to low-salinity and lower-mesohaline communities, while diatoms became increasingly dominant toward the middle- to high-salinity sections.
To examine community–environment relationships, we further separated the broad salinity organization from regional environmental controls by combining redundancy analysis and partial redundancy analysis. Salinity was the dominant background gradient structuring phytoplankton community differentiation at the continuum scale, marking a clear transition in community composition from the low-salinity estuarine section to the high-salinity bay section. Once the effect of salinity was accounted for, temperature, turbidity, and nutrient stoichiometric variables, especially DIN:DIP and DSi:DIN, remained significantly associated with community compositional differences, suggesting that seasonal thermal conditions, the underwater light environment and nutrient structure further regulate phytoplankton communities under comparable salinity backgrounds. The Zhangjiang Estuary captured the transition from multi-group co-dominance to increasing diatom dominance, whereas Dongshan Bay mainly showed seasonal fluctuations and among-station variability within a high-salinity bay setting. Our study provides an integrated, multi-seasonal view of phytoplankton community organization in a subtropical estuary–bay continuum, and highlights the importance of distinguishing broad salinity organization from regional environmental controls for interpreting high-resolution spatial and temporal changes in coastal plankton communities.

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