Bottom sediments of harbors in the South Korea have been long suspected for metal contamination due to ship-based and urban-based activities for the past several decades. A number of areas have been suspected to impair ecosystem services to the local residents and drawn complaints from main stakeholders. Twelve contamination suspected harbors were subject to evaluate the level of contamination of Cr, Ni, Cu, Zn, As, Cd, Pb and Hg. The level of sediment contamination for each metal was evaluated comparing the relative enrichment of a given metal to pollution-insensitive aluminum. Regional background concentration of a given metal was also determined based on its down core measurement and sediment texture. Ecological risk posed by the presence of heavy metals was evaluated using the sediment quality guidelines (SQGs) developed by United States National Ocean and Atmosphere Administration (US NOAA) as benchmarks for evaluating sediment chemistry to aquatic organisms. Cu, Zn, Cd, Pb and Hg in the surface sediment were found to be higher than a factor of 1.5 than background sediments, and the overall metal contaminations of surface sediment can be regarded as medium-high- to high-priority sites in the sense of SQGs.