To investigate the spatiotemporal characteristics of periphytic algae community structure and the Benthic Index of Biotic Integrity (B-IBI) in the Jinsha River, this study conducted two sampling surveys on periphytic algae and physicochemical factors at 15 representative sampling sites in November 2023 (dry season) and May 2024 (normal water period). Results showed that a total of 118 species of periphytic algae belonging to 59 genera and 7 phyla were detected, including 48 species from 5 phyla in the dry season of 2023 and 95 species from 6 phyla in the normal water period of 2024. Spatially, the distribution trends of total species richness and abundance of periphytic algae were basically consistent, both showing a gradually increasing trend from the downstream reservoir section of the Jinsha River to the upstream conservation section of the Yangtze River. Temporally, both the abundance and species richness of periphytic algae in the normal water period were higher than those in the dry season. Overall, the physicochemical indices of the Jinsha River water showed a decreasing trend from the reservoir areas to the river channels, with slightly higher values in the normal water period than in the dry season. Through parameter value distribution range analysis, discriminant ability analysis, and redundancy analysis of candidate parameters, the B-IBI index system for the study area was determined. The baseline values of the periphytic algae integrity index were 6.04 in the dry season of 2023 and 6.62 in the normal water period of 2024. The water ecological health status of the conservation section of the upper reaches of the Yangtze River is generally in a healthy state, and the overall water ecological health status gradually improves with the increase of the distance from the cascade reservoirs in the lower reaches of the Jinsha River.

Phytoplankton communities in the proposed water source area of the Western Route of the South-to-North Water Diversion Project showed multi-level responses across monitoring-period groups and diversion areas. Based on 64 valid samples, total biomass ranged from 0.027 to 5.659 mg L⁻¹ and showed no consistent differences between monitoring-period groups or diversion areas, indicating site- and sampling-period-scale patchiness. Among the dominant biomass-contributing taxa, most were diatom taxa, and the relative contributions of the top ten dominant taxa and Other taxa were reorganized among monitoring-period–area combinations. NMDS, PERMANOVA, and PERMDISP showed that monitoring period was significantly associated with community structure, whereas diversion-area effects were not significant. dbRDA indicated significant environmental–spatial constraints on community composition, with an adjusted explanatory power of 28.2%; T, NH₄⁺–N, TN, NO₃⁻–N, EC, pH, DO, and DTN were significant predictors. VPA showed stronger pure environmental than pure spatial effects, while DDR and EDR revealed significant geographic and environmental distance relationships. Taxonomic Bray–Curtis null models suggested a predominance of stochastic-like taxonomic turnover signatures, with stronger deterministic-like deviations in the upper-line diversion area. GAM identified NH₄⁺–N, DO, and EC as significant biomass predictors. These findings support integrating biomass, community composition, measured physicochemical variables, and taxonomic assembly signatures into sustainability-oriented phytoplankton monitoring for high-elevation riverine water source areas, thereby providing ecological evidence for sustainable water source protection and adaptive management.