Introduction: River-influenced continental shelves impose strong seasonal nutrient pressure on phytoplankton assemblages, yet the environmental regulation of phytoplankton assemblages in the outer estuarine zone, and the way their dynamics propagate to higher trophic levels, remains poorly resolved. Methods: We conducted three cruises in spring, summer, and autumn 2024 at 28 stations in the exclusive economic zone (EEZ) adjacent to the Yangtze River Estuary, characterizing the phytoplankton community together with water quality, surficial sediment geochemistry, and the accompanying zooplankton and macrobenthos as ecosystem context. Results: The phytoplankton community was strongly seasonal and near-monodominant in summer: the diatom Skeletonema costatum contributed 76.3% of total cell density in spring and 98.4% in summer, then collapsed to 0.7% in autumn, when diversity rose as dominance dispersed among larger diatoms; cell density declined by three orders of magnitude from spring to autumn. These shifts tracked the physicochemical environment. Dissolved inorganic nitrogen exceeded the Class I seawater criterion in 53.6% of spring–summer observations, dissolved inorganic phosphorus exceedance peaked in autumn at 89.3%, and summer bottom-water dissolved oxygen fell to 2.10 mg L−1, consistent with regional hypoxia; trace metals remained below Class I sediment criteria. Zooplankton biomass peaked in summer, whereas macrobenthic standing stock declined 14-fold from summer to autumn, with three stations azoic. Canonical correspondence analysis retained dissolved oxygen and temperature across all biological groups, while nutrient variables were retained only for the planktonic communities. Discussion: The phytoplankton community thus emerges as the most environmentally responsive component of this shelf ecosystem, underscoring the value of integrated, multi-season monitoring of net-collected microalgal assemblages to support coastal management.

Large-scale fishing bans are increasingly implemented to restore aquatic ecosystems, yet their effects on lower trophic levels remain poorly understood. As one of the world’s largest estuarine systems, the Yangtze River Estuary has been subjected to a ten-year fishing ban since 2021, providing a unique opportunity to potentially examine the response of plankton community to reduced fishing pressure along a steep salinity–nutrient gradient. This study relies on one-off environmental and plankton field surveys conducted in autumn 2024 (a sampling instead of multi-year time-series monitoring), we applied redundancy analysis, Mantel tests, and threshold indicator taxa analysis to tentatively clarify the roles of nutrients and salinity in structuring post-ban plankton communities. Species richness may have increased substantially compared with pre-ban levels, but community evenness declined and the dominance of Skeletonema costatum could have intensified, revealing a possible non-equilibrium recovery pattern. Zooplankton density increased substantially, which may not be fully consistent with the expectation under a simple top-down release scenario. Threshold analysis showed that S. costatum exhibited bidirectional responses to dissolved inorganic nitrogen and phosphate, with its positive response thresholds matching ambient nutrient concentrations in the inner estuary; this discrepancy is only a plausible inference since we lack direct measurements of fish predation and zooplankton grazing rates to verify causal trophic interactions. Our findings suggest that bottom-up forces driven by persistent eutrophication remain the dominant control on plankton community structure three years after the ban. From a watershed management perspective, our observational results provide a tentative implication that substantial reductions in nutrient loading might be required to mitigate unbalanced plankton community recovery; otherwise, the structural integrity of plankton assemblages could lag far behind the recovery of species richness under the current eutrophic background.

The Changjiang Estuary is a major hotspot for harmful algal blooms (HABs) in China. Metabarcoding analysis was conducted during four seasonal cruises (March, August, October 2025, and January 2026) at 14 stations to reveal the composition, dynamics, and environmental drivers of harmful algal bloom species in this region. A total of 63 HAB species were detected, with diatoms dominating year-round but dinoflagellates increasing markedly from spring (21.6%) to summer and autumn (34.8–44.6%). Salinity emerged as the primary factor structuring spatial patterns: the euryhaline diatom Skeletonema costatum dominated low-salinity nearshore waters, whereas diverse dinoflagellates, including Karlodinium veneficum, Prorocentrum micans, Heterocapsa rotundata, and Alexandrium catenella, prevailed offshore. Seasonally, the diatom-to-dinoflagellate ratio declined from 10.6 in spring to 1.6 in autumn, coinciding with rising temperature and declining N:P ratios. Notably, most high-abundance dinoflagellates are mixotrophic, a trait that likely confers competitive advantages. Our findings demonstrated that HAB species dynamics were shaped by the interplay between salinity-driven habitat filtering and trophic functional traits, advocating for the inclusion of mixotrophy as a key criterion in future HAB monitoring and early warning frameworks. Future monitoring would benefit from integrating these molecular trends with classical quantitative methods for validation.