Abstract: The composition of benthic algal communities is closely related to the health status of river ecosystems.Analyzing the composition of benthic algal communities can provide a theoretical basis for protecting the aquatic ecological health of rivers.Taking the Chishui River, a first-level tributary of the Yangtze River without damming on the main stream, as an example, benthic algae at 26 sampling points along the Chishui River main stream were sampled and surveyed in March, July, and November 2023.A benthic algal biological integrity index (Pe-IBI) was constructed with core parameters including total unit score, Shannon-Wiener index, and cell density.The 95th percentile of Pe-IBI values from all sampling sites was selected as the optimal value, and it was equally divided into five sections, in which a section closest to the 95th percentile represented the best ecological status, and was defined as the ecological baseline for the Chishui River (dry season 5.53, wet season 6.01, normal season 6.37).This baseline was used to evaluate the river′s ecological health in 2023.Principal component analysis (PCA) and correlation analysis were used to select DO, EC, DTN, TP, and NH₃-N as the main environmental factors from 17 environmental factors.Generalized additive models (GAM) and redundancy analysis (RDA) were used to analyze the relationships between the core Pe-IBI parameters (cell density, Shannon-Wiener index, total taxonomic units) and the primary environmental factors.The results showed that when DO concentration exceeded 10 mg/L, cyanobacterial cell density was positively correlated with DO.When EC was less than 420 μs/cm, the cell density of benthic algae increased with increasing EC.As TP concentration increased, the cell density of cyanobacterial increased rapidly.When TP, DO, EC, and NH₃-N increased, the Shannon-Wiener index decreased, leading to a decrease in benthic algal biodiversity.