The Three Gorges Reservoir (TGR) holds the distinction of being China's largest reservoir, and the presence of pollutants in the fish from the reservoir have a direct impact on the health of local residents. Thus, 349 fish specimens of 21 species and 1 benthos (Bellamya aeruginosas) were collected from four typical tributaries of the TGR from 2019 to 2020. These specimens were analyzed for the concentrations of total mercury (THg) and methylmercury (MeHg), and some representative samples were tested for δ13C and δ15N values to reveal the characteristics of bioaccumulation and biomagnification. The maximum safe daily consumption was estimated based on the oral reference dose (0.1 μg kg−1 bw/day according to US-EPA, 2017). The results showed that the mean THg and MeHg concentrations in fish from the TGR tributaries were 73.18 ± 49.21 ng g−1 and 48.42 ± 40.66 ng g−1, respectively, with the trophic magnification factors (TMFs) of THg and MeHg being 0.066 and 0.060, respectively. Among all the fish species in the tributaries, the highest daily maximum safe consumption amount was 1253.89 g for S. asotus consumed by adults, while the lowest was 62.88 g for C. nasus consumed by children.