To explore the characteristics of the phytoplankton community and environmental driving mechanisms in arid river basins, a systematic investigation of phytoplankton was conducted in May 2023, focusing on three sections of the Kuye River basin (upstream: Wulanmulun River; tributary: Beiniuchuan River; downstream: Kuye River mainstream). A total of 60 species of phytoplankton were identified, belonging to six phyla and 41 genera, with Bacillariophyta and Chlorophyta as the dominant phyla. Significant differences in species diversity were observed among the three river sections, with the highest diversity in the Wulanmulun River and the lowest diversity in the Beiniuchuan River. The water quality index (WQI) showed the best water quality in the Beiniuchuan River and the worst in the Wulanmulun River. Notably, Ankistrodesmus spiralis and Ankistrodesmus acicularis were reliable indicators for evaluating water quality in the Kuye River basin. Redundancy analysis highlighted that conductivity (COND), water temperature (WT), and dissolved organic carbon (DOC) were key physicochemical factors shaping the phytoplankton community in this basin. Correlation analysis further indicated that the Scenedesmus dominant in the mainstream of the Kuye River was mainly affected by dissolved oxygen (DO) and nitrate-nitrogen (NO₃⁻-N); Cyclotella and Gomphonema abundant in the Wulanmulun River were mainly affected by NO₃⁻-N, ammonium-nitrogen (NH₄⁺-N), and the nitrogen/phosphorus ratio (N/P); while Diatoma, which prevailed in the Beiniuchuan River, was mainly affected by COND.