Concentrations of Ni, Cd, Pb, Cu, and Zn were measured in the surface sediments of Mejillones Bay at 32 sites ranging in depth from 10 to 95 m. A similarity dendrogram analysis separated the study area into two large sedimentary facies: a coastal zone with low metal concentrations and a deep zone with high metal concentrations. The abundances of Zn, Ni, and Pb increased between two sampling periods (5 years apart) in association with greater anthropogenic activity along the coastline of the bay at the present. The results were analyzed with the index of geoaccumulation and by applying the sediment quality guideline. Although similar to preindustrial levels, current Cu and Ni concentrations pose a likely threat to communities of benthic organisms. Concentrations of Zn and Pb are enriched, probably in connection with the industrial development of the zone, but do not reach dangerous levels for the benthic communities. Cd concentrations are toxic to benthic life, even though those measured herein are similar to preindustrial levels. Thus, these Cd levels are a result of the bay's natural characteristics (e.g., high biological productivity, the microxic water-sediment interface). The results of the Chilean aquatic sediment quality standards and the international standard (sediment quality guideline) were similar but differed from those found using the index of geoaccumulation, which suggests that the proposed reference values for Chilean aquatic sediment should be reviewed.