Abstract Tropical cyclones (TCs), as natural extreme weather events, alter plankton and hydrological environments, affecting the stability of biological processes in freshwater ecosystems, and such TC effects vary with water depths. Previous studies have found increased phytoplankton biomass resulting from TC effects has been observed, leading to potential strong grazing of zooplankton and enhanced plankton trophic‐level relationships. However, this remains understudied, particularly under in situ conditions. Using a zooplankton to phytoplankton (ZB/PB) ratio to represent the plankton trophic‐level relationship, we estimated the ZB/PB ratios at various depth intervals, including surface (2 m depth) and euphotic (depths between 0 and 20 m) depths and depth layer 0–50 m (depths between 0 and 50 m), in a subtropical deep oligotrophic freshwater ecosystem from 2012 to 2015 to understand how TC effects would influence changes in the ZB/PB ratio variations. TCs affected the surface and euphotic ZB/PB ratios but not those at the depth layer 0–50 m. The TC durations had an initially negative and then positive impact on the surface ZB/PB ratio, indicating that slow‐moving TCs might restructure surface plankton trophic‐level relationships. The water temperature and nutrient dynamics during the TC weeks showed the highest correlations with the ZB/PB ratios at the surface and euphotic depths. The combined environmental effects influenced the ZB/PB ratios at the surface and euphotic depths during the TC weeks, with 65.1% and 72.2% of the total variations explained in the multivariate regressions, respectively. There were greater impacts of TCs in shallow water (surface and euphotic depth) than in deep water. Aquatic food chains may be unexpectedly vulnerable to natural extreme weather events, such as TCs, and continuous assessments of food chain dynamics are necessary to better manage potential risks from natural extreme weather events in freshwater ecosystems.
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