In this study, the longitudinal distribution of heavy metals (including As, Cd, Cr, Cu, Ni, Pb, and Zn) from sediment of a 70-km long canyon reservoir in Yunnan Province was investigated and their potential ecological risks were assessed. The results indicated that the concentration of all the detected metals in the sediments that was sampled near the dam was much higher than that sampled from upstream far from the dam. The geoaccumulation index (I(geo)) and contamination factors (CF) suggested that Cd was the most important contamination factor, followed by As and Zn, while the concentration of Cr, Cu, Ni, and Pb was at uncontaminated levels. Cd posed a high potential ecological risk in the sediment. Furthermore, potential ecological risk is significantly correlated with the distance from the dam.