Abstract: The Benthic Index of Biotic Integrity (B-IBI) has been widely used to assess the ecological health of river ecosystems. Based on an analysis of the impact of shoreline utilization types on benthic community structure, this study used B-IBI to evaluate the ecological health of the northern Jiangsu section of the Beijing-Hangzhou Grand Canal (the source area of the East Route of the South-to-North Water Transfer Project). It also applied Redundancy Analysis (RDA) to explore the main environmental factors influencing the ecological health of this section of the Grand Canal. The results showed that 33.3% of the river segments in the northern Jiangsu section of the Beijing-Hangzhou Grand Canal were in a healthy state, while 40.0% were in poor or lower conditions. The spatial distribution of health status showed a pattern where the northern sections were in better condition than the southern ones. Natural shoreline segments provided more favorable habitats for benthic organisms, with significantly higher benthic community diversity and better ecological health compared to artificial shoreline segments. RDA results indicated that the proportion of natural shoreline, conductivity, and ammonia nitrogen were the key factors influencing the ecological health of this section of the Grand Canal. This study provides scientific support for shoreline protection and ecological restoration in the northern Jiangsu section of the Beijing-Hangzhou Grand Canal.