To assess the heavy metal pollution in Changshou Lake, sediments were collected from nine sites at three periods (dry, normal, and wet) in 2013. The Hg, As, Cr, Cd, Pb, Cu, and Zn levels were then determined. The index of geoaccumulation (I geo) and the sediment pollution index (SPI) were applied to the sediment assessment, and Pearson's correlation analysis and factor analysis (FA) were performed to identify common pollution sources in the basin. The results showed that heavy metals presented significant spatial variations with Cr, Cd, Pb, Cu, Zn, Hg, and As concentrations of 29.66~42.58, 0.62~0.91, 24.91~37.96, 21.18~74.91, 41.65~86.86, 0.079~0.152, and 20.17~36.88 mg kg(-1), respectively, and no obvious variations were found among the different periods. The average contents of the metals followed the order Zn > Cu > Cr > Pb > As > Cd > Hg, which showed a high pollution in the sediments collected from open water and at the river mouth. The assessment results indicated that toxic heavy metals presented obvious pollution with I Hg of 0.64~1.36 (moderately polluted), I Cd of 1.66~2.22 (moderately to heavily polluted), and I As of 1.21~2.07 (moderately to heavily polluted). The heavy metal pollution states followed the order Cd > As > Hg > Cu > Pb > Zn > Cr, and the SPI showed that the sediment collected from open water area was more polluted than those obtained from the tributaries and the river mouth. Cr, Cd, Hg, Pb, Cu, As, and Zn were mainly attributed to sediment weathering with Hg, Pb, and Cu and partially due to domestic sewage from the upper reaches. These results indicate that the more attention should be paid to the inner loads of sediment in order to achieve improvements in reservoir water quality after the control of external pollution.