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The Yangtze River deepwater channel in the downstream of Nanjing China is the largest water transport project. It necessitates an effective ecological risk assessment of sediment–bound heavy metals driven by construction of the Yangtze River ship channel. We conducted a three–year field studies to investigate levels of heavy metals (Hg, Cd, Pb, Cu, and Zn), pH, and total phosphorus in sediments, as well as diversity of zoobenthos, phytoplankton, and zooplankton along the Taichang–Nantong reaches of the Yangtze River. Results showed that high–concentrations of Pb is at 130.62 mg/kg and of Hg is at 0.88 mg/kg in the sediments, which mainly emitted from the power electronics, power systems, and the hydrocarbon–based fuel combustion via principal component analysis. Based on optimized contamination indices for metals, we should consider their ecological risks when the potential ecological risk factor (E r i) of Hg is up to 210 in the basin. The channel construction resulted in significantly increasing concentrations and ecological risks of heavy metals at the lower reaches. Meanwhile, the community structure of aquatic organisms changed and the investigated species richness decreased significantly from 78 to 47 during the project. Through redundancy analysis, more significant variances of the plankton species richness (55% and 22%) were attributed to E r i of heavy metals and their combined risk index as compared with both planktonic and benthic organisms (52% and 17%). Moreover, the species density of both Melosira granulata and Navicula sp., major phytoplankton species in the basin, were significantly negatively correlated to Pb and Hg in sediments. Plankton was more sensitive indicators than zoobenthos due to the ability of plankton to reactivate and bioaccumulate sediment–bound heavy metals. This study innovatively warned management to control river engineering–induced ecological risks of metals in sediments and revealed their potential risk pathway of ingestion by sensitive plankton. Image 1 • Both pollution sources and toxicity mechanisms were identified to control risks. • Heavy metal risks were evaluated based on optimized ecological risk factors. • Ship channel construction cause impacts of heavy metals on aquatic ecosystem. • Community structural change was linked to risks posed by Hg and Pb in sediments. • Plankton were more sensitive than zoobenthos by ingestion of metals in sediments. [ABSTRACT FROM AUTHOR]