Heavy metal assessment in Dakhla Bay (Atlantic coast) was carried out using different environmental and ecological indices. Heavy metal concentrations were measured using ICP–AES and were compared with consensus-based sediment quality guidelines. The distribution of heavy metal concentrations varies for the three groups: (i) lead distribution is dominated by its associations with copper and chromium. These elements have the same source, most probably related to anthropogenic activities. (ii) Nickel, zinc and cobalt are associated with aluminium and iron indicating their terrigenous origin (natural content), and (iii) cadmium concentration is related to upwelling currents. This paper systematically studied the distributions and pollution levels of heavy metals in sediment in the coastal areas in Dakhla Bay, which is of scientific significance, to discuss the changing rules and the affecting factors of the harmful heavy metals and can be adopted for reference to other coastal areas.