<p>Clarifying the succession and response mechanisms of water quality and phytoplankton communities is crucial for river water environment management. However, research in this field remains relatively insufficient in certain hilly areas of inland basins. This study conducted seasonal sampling in the Yaoshi River, analyzed water chemistry parameters and phytoplankton composition, and applied multivariate statistical methods to assess the water quality characteristics and phytoplankton structure. First, a descriptive statistical analysis of 13 water chemistry parameters revealed that the river is primarily affected by organic pollution. A total of 152 species of phytoplankton from 6 phyla were identified, with Cryptophyta showing the highest abundance in spring, Cyanophyta dominating in summer, and Bacillariophyta prevalent in autumn–winter. Further correlation and redundancy analysis (RDA) indicated varying degrees of association between phytoplankton community diversity, biomass, abundance, and water quality parameters. On an annual scale, water temperature was identified as the primary driver of phytoplankton community succession. However, during the high-temperature period, the nitrogen-phosphorus ratio became the dominant factor. The results revealed that the sensitivity of phytoplankton to total phosphorus (TP) decreased due to long-term adaptation to high-phosphorus environments, while total nitrogen (TN) became a key limiting factor in the summer. Based on these findings, a combination of emergency measures and long-term strategies is recommended to improve river ecosystem health. This study provides a deeper understanding of the mechanisms behind water quality and phytoplankton dynamics in data-scarce basins and offers valuable insights for regional water environment policy development.</p>