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Since July 2022, the Yangtze River basin has experienced the most severe hydro-meteorological drought since record collection started in 1961, which has greatly affected the ecological environment of the Dongting Lake (DTL) basin. To investigate the effects of drought events on the eutrophication and phytoplankton community structure of DTL, the lake was sampled twice in August and September 2022 based on the water level fluctuations resulting in 47 samples. Furthermore, we combined the comprehensive trophic level index (TLI) and phytoplankton Shannon–Wiener diversity index (H) to characterize and evaluate the eutrophication status. The key influencing factors of the phytoplankton community were identified using redundancy analysis (RDA), hierarchical partitioning, and the Jaccard similarity index (J). Our results showed that the TLI of DTL changed from light–moderate eutrophication status (August) to mesotrophic status (September), whereas the H changed from light or no pollution to medium pollution. The phytoplankton abundance in August (122.06 × 104 cells/L) was less than that in September (351.18 × 104 cells/L) in DTL. A trend in phytoplankton community succession from Bacillariophyta to Chlorophyta and Cyanophyta was shown. The combination of physiochemical and ecological assessment more accurately characterized the true eutrophic status of the aquatic ecosystem. The RDA showed that the key influencing factors in the phytoplankton community were water temperature (WT), pH, nitrogen and phosphorus nutrients, and the permanganate index (CODMn) in August, while dissolved oxygen (DO) and redox potential (ORP) were the key factors in September. Hierarchical partitioning further indicated that temporal and spatial variations had a greater impact on the phytoplankton community. And the J of each region was slightly similar and very dissimilar, from August to September, which indicated a decreased hydrological connectivity of DTL during drought. These analyses indicated that the risk to the water ecology of DTL intensified during the summer–autumn drought in 2022. Safeguarding hydrological connectivity in the DTL region is a prerequisite for promoting energy flow, material cycle, and water ecosystem health. [ABSTRACT FROM AUTHOR]