The sediment acts as not only sink but also source of heavy metals in aquatic environment, which may cause the endogenous pollution in drinking water reservoirs. In this work, we collected the surface sediments from Qingcaosha Reservoir, the largest river-embedded reservoir in China, and investigated the spatial distribution, risk, and sources of heavy metals in four seasons. Significant spatial and seasonal heterogeneity could be found in the distribution of five heavy metals (Cr, Cu, Mn, Zn, and Ni) in the surface sediments. The highest concentrations of the five metals were detected in the sediments from the reservoir downstream, especially in summer and next spring. The geo-accumulation index (I_geo) and enrichment factor (EF) suggest that the sediment pollution caused by single metal was heavier in summer than in other seasons. Also, the Nemerow pollution index (PI_N) manifests that the synergetic pollution induced by five metals was most serious in summer, followed by next spring. However, the potential ecological risk index (PERI) indicates that none of these metals caused potential ecological risk in four seasons. Comprehensive analysis demonstrates that the sediment pollution gradually increased from autumn to winter and then to next spring. Principal component analysis shows that the main pollution source of five heavy metals may come from industrial wastewater and domestic sewage, which was almost independent of seasons. This work can provide data support for the subsequent seasonal optimization of drinking water quality and reservoir management.