Abstract: The construction of cascaded reservoirs is a pivotal strategy for global water resource utilization, hydropower generation, and flood control. However, the cumulative effects of cascaded reservoirs, including river fragmentation, alteration of natural flow regimes and sediment retention, pose significant threats to the structure and function of riverine ecosystems.To investigate the impact of cascade reservoir construction on riverine aquatic ecosystems and to provide technical and data support for ecological monitoring, early warning, protection, and restoration, this study employed the Phytoplankton Index of Biotic Integrity (P-IBI) to assess the aquatic ecological health of the Tongzi River at 9 sampling sites from March to May 2024. Based on three aspects—phytoplankton community diversity, species richness, and evenness—20 candidate indicators were analyzed in terms of their distribution range, discriminative power, and Pearson correlation, resulting in the selection of seven core indicators: the number of Bacillariophyta taxa, Shannon-Wiener diversity index of phytoplankton, phytoplankton evenness index, phytoplankton richness index, cell density, the percentage of Chlorophyta cell density, and dominant species cell density. These parameters were used to construct a spring-specific P-IBI evaluation system for the Tongzi River. A ratio-based method was applied to establish a five-tier grading standard: Excellent, Good, Fair, Poor, and Very Poor, corresponding to the health status of the ecosystem. The results revealed that, during spring, a total of 77 phytoplankton genera from 7 phyla were identified in the cascade reservoirs of the Tongzi River. These included 29 genera of Chlorophyta, 25 genera of Bacillariophyta, 14 genera of Cyanophyta, and 4 genera of Euglenophyta. The phytoplankton community was predominantly of the Bacillariophyta-Chlorophyta-Cyanophyta type, with Bacillariophyta as the dominant group. Overall, the aquatic ecosystem of the Tongzi River during spring was found to be in a sub-healthy state. A distinct spatial trend was observed: ecological health conditions improved progressively from upstream to downstream, with downstream sites exhibiting better ecological status. Among the nine sampling sites, 1 site was classified as “fair”, 5 as “sub-healthy”, and 3 as “healthy”. The construction of cascade reservoirs exerted a noticeable influence on the river’s aquatic ecological health. Significant differences in phytoplankton community structure were observed between upstream and downstream of dams and among reservoirs, with P-IBI scores generally lower upstream of dams. Furthermore, P-IBI parameters showed significant correlations with key physicochemical factors such as pH, chlorophyll-a concentration, and the permanganate index, indicating that P-IBI has potential as an effective indicator of water quality pollution in the Tongzi River. Based on these results, it is strongly recommended that water resource managers authorities strengthen efforts to control pollution sources within the watershed, particularly in the upstream and reservoir regions. Moreover, optimizing the operation schedules of the cascaded reservoirs to mimic more natural flow patterns and enhancing wastewater treatment systems in the surrounding areas are critical steps toward mitigating ecological impacts and restoring the Tongzi River's aquatic ecosystem to a healthier state.