Hulun Lake, northern China’s largest semi-arid grassland lake, faces escalating cyanobacterial bloom risks under climate-driven hydrological extremes. This study investigated how a heavy rainfall event (30–31 July 2021) restructured phytoplankton communities across river-estuary-lake gradients, using pre- and post-rainfall sampling (28 July 2021 and 3 August 2021). Among 96 phytoplankton species (eight phyla, 20 functional groups), Cyanobacteria-dominated functional groups M (Microcystis spp.) and H1 (Anabaena circinalis and Aphanizomenon gracile) surged post-rainfall, increasing their combined biomass share from 23.79 % to 46.21 % in the estuary and 47.83 % to 76.2 % in the lake. Total biomass and chlorophyll-a (Chl-a) followed lake > estuary > river gradients, with lake Chl-a rising from 30.14 to 40.58 μg L–1 post-rainfall, indicating a heightened risk of bloom proliferation. Hydrodynamic disturbances reduced light availability, suppressing α-diversity in the lake while amplifying biomass via terrestrial nutrient influx. Spatially, post-rainfall α-diversity peaked in the estuary but declined sharply in the lake. Nutrient enrichment post-rainfall enhanced cyanobacterial competitiveness, while diversifying environmental pressures constrained competitive adaptability for non-cyanobacterial functional groups. These dynamics underscore synergistic risks of extreme rainfall and eutrophication in semi-arid lakes, where pulsed nutrient loading can override hydrodynamic stressors to fuel cyanobacterial dominance. To mitigate bloom risks, we recommend adaptive basin management prioritizing watershed nutrient control, high-frequency monitoring of hydrodynamic-nutrient interactions, and emergency measures for extreme rainfall scenarios.
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