Danjiangkou Reservoir is the biggest artificial reservoir in China. But spatiotemporal distribution and risks of metal(loid)s in it were still unclear after the operation of Middle Route of South-to-North Water Diversion Project. In this study, distribution pattern of fifteen metal(loid)s in the Danjiangkou Reservoir was investigated. It was shown that metal(loid)s concentrations in the water were much lower than the drinking water quality standards in China, while Sb, Co, Cd and Cr were identified as the major pollutants in the sediments. Environment–metal(loid)s correlation analysis revealed total organic carbon, sulfate, temperature, dissolved oxygen and total phosphorus markedly controlled metal(loid)s distribution in the water, while organic carbon, total phosphorus and ammonia nitrogen shaped their distribution in the sediments. Results of risk assessment further revealed that the sediments of Danjiangkou Reservoir were minor to moderate polluted, and Sb, Cd exhibited the highest potential ecological risk. Additionally, source identification showed agricultural activities (25.3%), industrial and mining activities (17.5%) and natural processes (57.2%) were the dominant sources of metal(loid)s burden in the sediments. Overall, the results are of significance to understanding the ecological risk and pollution sources in the Danjiangkou Reservoir, which is essential for the effective management of metal(loid)s pollution.