Abstract: During flood seasons, floods often have a significant impact on the water quality of lakes and reservoirs, and the influence of floods on water quality and algal communities needs in-depth exploration.This study employed partial Mantel tests and redundancy analysis to examine the distribution characteristics of phytoplankton and their driving mechanisms in the Danjiangkou Reservoir following the flood season floods in 2021.The results indicate that the autumn flood in 2021 had a considerable impact on the water quality of the Danjiangkou Reservoir, leading to differences in water quality and algal density between the Han Reservoir and the Dan Reservoir.The autumn flood caused an increase in turbidity in the Han Reservoir, resulting in a lower average algal density compared to the Dan Reservoir.After the autumn flood, a total of 15 species of phytoplankton were identified in the Danjiangkou Reservoir, primarily dominated by diatoms, cryptophytes, and dinoflagellates, indicating a mesotrophic state.The average algal density in the reservoir was 2.11×10⁵ cells/L.In the Han Reservoir, the algal composition was mainly diatoms, dinoflagellates, and cryptophytes, with dinoflagellates the most dominant (41.67%).In contrast, the Dan Reservoir was dominated by diatoms, cyanobacteria, and cryptophytes, with cryptophytes the most prevalent (67.18%).The algal communities in the Dan Reservoir were primarily driven by nitrogen and organic matter, whereas those in the Han Reservoir were influenced by multiple water quality factors, including nutrients, turbidity, and pH.The impact of the autumn flood was more pronounced in the Han Reservoir than that in the Dan Reservoir, and turbidity is the main driving factor for changes in algal communities in the Han Reservoir.