The Three Gorges Project (TGP) is the largest hydropower station ever built in the world. A better understanding of the concentrations of heavy metals in the aquatic environment of the Three Gorges Reservoir (TGR) is crucial for national drinking water security and sustainable ecosystem development. To thoroughly investigate the impact of heavy metals on water quality after the impoundment to the maximum level of 175 m in the TGR, the concentrations of the dissolved heavy metals (Cr, Cu, Zn, Cd, Pb, As) were measured in April and August 2015, by inductively coupled plasma mass spectrometry (ICP-MS). (1) Except Zn and Pb, most of the heavy metal concentrations in the water of the TGR reached the level of the National Surface Water Environmental Quality Standards (GB3838-2002) I of China, revealing that the water quality of the TGR was good overall. (2) There were significant positive correlations among the concentrations of Cu, As, and Cd, revealing that they may exhibit similar geochemical behaviors. (3) The spatial distribution of the heavy metal concentrations was diverse and complex. The Zn concentration obviously increased in the rainy season from upstream to downstream in the Yangtze River, while the other heavy metals exhibited no significant changes in their concentrations. The distribution characteristics of the heavy metal concentrations on both sides and the middle of the river were different at different sites. (4) The health risk of the six elements was assessed through a human health risk assessment (HHRA), and the assessment results were lower than the maximum acceptable risk level designed by the US EPA and International Commission on Radiological Protection (ICRP). The HHRA model in the aquatic environment revealed that the risk of non-carcinogenic heavy metals (Cu, Zn, and Pb) was at a negligible risk level of 10⁻¹¹∼10⁻⁹ a⁻¹. At all the study sites, the risk of carcinogenic heavy metals (Cr, Cd, and As) was higher than the risk of non-carcinogenic heavy metals. As was the most important risk factor, followed by Cr. The results of this study hold great significance for a timely understanding of the changing water quality for affected departments to ensure the health of the residents in the TGR area.