Accumulated heavy metals in surface sediments are released into the aquatic environment, causing secondary contamination of the hydrosphere, and increasing the risks to human health. To evaluate the pollution characteristics of heavy metals in the sediments of the Chishui River Basin, in the present study, the concentrations of five heavy metals in surface sediments of the Chishui River Basin in China were investigated using the geo-accumulation index, pollution load index, and potential ecological risk indexes. These indexes evaluated the degree of contamination and the influence of human activities on heavy metal levels in the basin. Cu, Zn, Cd, Hg, and As were found at concentrations of 5.12–120.40, 36.01–219.31, 0.03–1.28, 0.01–1.18, and 1.56–11.59 mg kg^–1, respectively, with mean values of 37.43, 91.92, 0.25, 0.07, and 5.16 mg kg^–1, respectively, in the order Zn > Cu > As > Cd > Hg. The contamination indices revealed Hg as the principal pollutant based on the spatial distribution, while Pearson’s correlation coefficients suggested that Cu, Zn, and As originated from a similar source. Hg had a different source from the other metals, whereas Cd originated from a different source compared with that of Zn, As, and Hg. This paper showed a Hg and Cd contamination in the Chishui River Basin.