Cu, Zn and Pb in sediments, and Cu and Zn in benthic organisms were analyzed in 7 coastal zones of San Jorge Bay, to evaluate the impact of the anthropogenic activities on marine ecosystem. High metal concentrations in sediments were found in Puerto Antofagasta. According to Cu concentrations measured in 14 species of benthic organisms, the bay can be distinguished in two sectors, a southern zone with high Cu content, and a northern zone with low Cu content. The Zn concentration was higher in Puerto, specifically, than others coastal zone of the bay. In general, the distribution of these metals in the bay suggest that anthropogenic activities developed in the coastal zone has an impact on metal content in marine sediments, and that the harbors of mineral loading suppose a risk to benthic communities. However, there is no evidence of metal bioaccumulation in the analyzed organisms in this work. On the other hand, only Argopecten purpuratus found in Puerto Antofagasta has Zn concentrations higher than that established level in the Chilean's health law.