Phytoplankton Dynamics in a River–Lake Continuum

River–lake transition zones are simultaneously influenced by riverine inputs and lake water, potentially making their phytoplankton communities strongly season dependent. To characterize spatiotemporal differentiation along the inflow continuum of a river-connected shallow lake, we surveyed 21 fixed sites in the inflowing Huangpen River (HPH), the river–lake transition zone (HS), and the main lake (SJH) of Shengjin Lake in spring, summer, autumn, and winter 2025, yielding 84 observations. Generalized estimating equations tested the effects of hydrological unit, season, and their interaction while accounting for repeated sampling. Community composition was evaluated using a restricted-permutation repeated-measures PERMANOVA, and partial redundancy analysis (pRDA) was conditioned on season with permutations restricted within sites. We recorded 245 phytoplankton taxa belonging to 106 genera and eight phyla. Except for TP, all water-environment variables and the algal-state indicator Chl-a showed significant hydrological unit × season interactions, indicating that differences among hydrological units were not constant throughout the year. Total abundance, taxon richness, and all diversity indices also exhibited significant interactions: HS and SJH had higher abundance in summer, whereas abundance in SJH declined sharply in autumn; the highest Shannon index shifted from HPH in spring to SJH in autumn. Season, hydrological unit, and their interaction explained 32.19%, 4.86%, and 10.02% of community variation, respectively (P = 0.0001), although within-group dispersion also varied among units and seasons. After conditioning on season, 10 external environmental variables jointly explained 13.77% of total community variation (adjusted R2 = 6.28%; P = 0.0001), but no marginal effect remained significant after false-discovery-rate correction. Thus, the Shengjin Lake inflow continuum did not exhibit a stable, unidirectional river-to-lake gradient throughout the year; algal accumulation and community-transition characteristics in the river–lake transition zone were strongly season contingent.