Dam construction has a far-reaching impact on trace metal accumulation and the metal-induced quality of the aquatic environment. However, the long-term impacts of dam construction and impoundments on the spatial distribution of trace metals and water quality remain poorly understood. Here, we found that the concentrations of trace metals in the mainstream water of the world's largest reservoir, Three Gorges Reservoir (TGR), decreased after impoundment, while their concentrations and contamination in the sediments of the water-level fluctuation zone increased significantly, especially for anthropogenic sources of metals such as cadmium, lead, and zinc. The spatial and temporal variations of anthropogenic metals in the sediments revealed increased anthropogenic dominance in their distribution under current hydrological management, especially for the urban area of the upper TGR. Sediment fluxes, particle composition, and extreme climate modulated the distribution of trace metals in the sediments. The results demonstrate that human activities have increasingly determined the distribution and contamination state of trace metals in the mainstream TGR. However, in contrast to our previously thought, the anthropogenic discharge of trace metals did not adversely affect water quality. Our results indicate that dam construction in riverine systems attenuates trace metal contamination in water through sediment sorting and deposition.