In order to promote the development of biodiversity, the present study conducted three sampling surveys at 26 representative sampling sites selected from the Chishui River, a freshwater river in China, in July (rainy season), November (flat water period), and April 2024 (dry season), respectively, focusing on the relationship between benthic algae and the response of water environmental factors. The results revealed that a total of 140 species from 48 genera and 7 phyla of benthic algae were identified, with the highest number of species belonging to the diatom phylum (85 species). The average density of benthic algae was highest during the flat water period, followed by the dry season and the flood season. Microcystis sp. was the dominant species during the flood season, while Gomphonema sp., Achnanthes tumescens, and Oscillatoria sp. were common dominant species during the dry and flat water periods. Achnanthes tumescens was the absolute dominant species in the upstream during the dry and flat water periods; Leptolyngbya sp. was the absolute dominant species in the midstream during the flat water period, and Oscillatoria sp. was the absolute dominant species in the middle reaches during the dry season. The Shannon-Wiener index, Margalef index, and species richness of benthic algae during the dry and flat water periods decreased from upstream to downstream. Non-metric multidimensional scaling analysis revealed significant differences in the community structures of benthic algae in the upper, middle, and downstream areas of the Chishui River during different periods, while cluster analysis indicated high similarity among benthic algae communities in locally adjacent areas. The differences in the benthic algae community structure increased with environmental and geographical distance, with environmental distance playing a greater role than geographical distance. RDA (Redundancy Analysis) identified TN (Total Nitrogen), TP (Total Phosphorus), DO (Dissolved Oxygen), EC (Electrical Conductivity), and NH3-N (Ammonia Nitrogen) as key water environmental factors influencing the structure of benthic algal communities in the Chishui River.
