In this study, 46 reservoirs in South Korea were characterized based on heavy metal concentration in sediments. We analyzed the relationship between heavy metal concentrations, physicochemical water quality and hydromorphological factors in each reservoir. Study reservoirs were classified into five groups of reservoirs, by hierarchical cluster analysis based on the similarities of heavy metal concentration. Group 1 had the most severe sediment heavy metal contamination among the groups, whereas Groups 2 and 3 showed low levels of heavy metal contamination. Group 4 displayed high value of Ni, and Group 5 showed high contamination of Pb, Cu, Cr, Ni, and Hg. Groups 1 and 5, which had high concentration of heavy metals in sediments, showed a high density of mines in the catchment of reservoirs. Heavy metal concentration was high in reservoirs with large capacity or the ones located at higher elevation, and also highly related with number of mines in the catchment of reservoir. This study can contribute to the systematic management of sediment heavy metals in reservoirs.