Three Gorges Reservoir (TGR) reached the maximum water level (175 m) of impoundment in Oct. 2010. In order to reveal the potential influence of the greatest water-level impoundment on the heavy metal pollution in the typical waters of TGR, the content level of trace metals ( Hg, Cd and Pb) in biota and potential biomagnification along the aquatic food chain were investigated in the main stem of TGR from July 2011 to August 2012, as well as the relationship between the trace metal concentrations of aquatic consumers (fish and aquatic invertebrate) and biological factors. Our study showed that no individual data of the three trace metals in biota exceeded the edible safety criteria of aquatic products in China and FAO. In contrast with those before the impoundment of TGR, Hg showed a little higher, while Cd and Pb exhibited a little lower level after the impoundment. Trace metals in TGR exhibited relatively lower concentrations compared with those in reservoirs in other countries. Significant correlations were found between the Cd concentration and body size (body length and body weight) of Cyprinus carpio, as well as the Hg concentration and body size (body length and body weight) of Erythroculter ilishaeformis. As for feeding habits, there was statistically significant difference between trace metal concentrations in herbivorous, planktonic, omnivorous and carnivorous fish. However, no significant difference was found between the metal concentrations in fish with different habitats (pelagic, mesopelagic and benthic). Even so, the overall trend was that fish living in benthic layer had higher heavy metal concentrations than those in pelagic and mesopelagic zones. The regression slopes of log-Hg concentration versus delta(15)N, served as an indicator of trophic magnification factor (TMF). Significant correlations (P < 0.05) were observed for Hg in the food web of TGR. TMF of Hg in TGR indicated lower level (0.046-0.066) in contrast with those in the reservoirs of United States and Canada, and this was explained by the relatively lower organic carbon in the soil and sediment of TGR.