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China’s Three Gorges Reservoir (TGR) is the largest water conservancy project in the world, and plays a significant role in flood control and water transport. To study the health status of the tributaries of TGR, we set up 175 sampling sites, including 15 reference sites and 160 impaired sites on 36 important tributaries of TGR, and collected zoobenthos at these sampling sites. We selected 26 candidate metrics, analyzed them in terms of the distribution range, discriminant ability and correlation. Eight core metrics (i.e., total taxa, ephemerida + trichoptera + plecoptera taxa, diptera taxa, ephemerida%, trichoptera%, Shannon–Wiener diversity index, dominant species% and filter%) were identified, and then the benthic indexes of biological integrity (B-IBI) was established. The B-IBI was then used to evaluate the ecological status of 36 tributaries of TGR. Among all the sampling sites, “excellent”, “good”, “fair”, “poor” and “very poor” accounted for 5.14%, 13.14%, 28.00%, 44.57%, and 9.14%, respectively. Among all streams and rivers, “excellent”, “good” “fair”, “poor” and “very poor” accounted for 5.56%, 41.67%, 50.00%, 2.78%, and 0%, respectively, showing a general good condition for all tributaries. There was a significant difference in health status between tributaries in the TGR dam and those in its upper reaches. The B-IBI established in this study can capture the health status of 36 important tributaries of TGR. This study does not only enrich the practice of health assessment using B-IBI, but also provides some reference for the evaluation of similar rivers across the world.

Health assessment of important tributaries of Three Georges Reservoir based on the benthic index of biotic integrity