Abstract: As the core area for intensive agricultural production, agricultural irrigation areas have been continuously influenced by intensive human activities such as irrigation system regulation, agricultural fertilizer application, and changes in land use patterns for a long time. The ecosystem structure and hydrological processes have exhibited significant human disturbance characteristics. Exploring the impacts of water environmental factors in this region on the structural characteristics and spatiotemporal changes in phytoplankton communities is of significant theoretical and practical importance for maintaining the stability of river ecosystems and promoting the sustainable use of water resources in intensive agricultural production areas. For this purpose, surface water and phytoplankton in the Xiaohe River Irrigation Area were sampled from June 2023 to April 2024, and phytoplankton characteristics and key water environmental factors were analyzed using correlation analysis, redundancy analysis, and other methods. The results showed that the surface water in the Xiaohe Irrigation Area was polluted to a certain extent, yet the diversity of phytoplankton remained high. A total of 94 species (including varieties) belonging to 54 genera and eight phyla of phytoplankton were identified in the study area, with five dominant species. The community structure and diversity index of phytoplankton showed significant spatiotemporal distribution characteristics. During the wet season, NO₃⁻-N, TP, pH, EC, SD, and TDS were the main water environmental factors affecting phytoplankton species in the Xiaohe River Irrigation Area, whereas during the dry season, T, TP, TN, and NO₃⁻-N were the main water environmental factors affecting the species characteristics in the study area. The results of this study contribute to a further understanding of the ecological characteristics of phytoplankton communities in the Xiaohe River Irrigation Area and provide a theoretical basis for the dynamic management of phytoplankton resources and water ecological protection in agricultural irrigation areas.