The superficial and cored sediments of the Sidi Moussa lagoon (Atlantic Moroccan coast) have been analysed in order to determine their main characteristics and their heavy metals contents. Two groups of metals can be distinguished: Al, Fe and Cu whose distribution is mainly governed by the intra-lagoonal dynamics. These contents are near of those of the natural geochemical background noise that underlines their natural origin. Zn, Cr and Ni have relatively more elevated contents than the natural geochemical background noise indicating human-made pollution. The geo-accumulation indicator shows that the Sidi Moussa lagoon is moderately polluted. The totality of results in this context compared to the standard values suggested by the Agency of Protection of the Environment of United States leads to the conclusion that the sediments of Sidi Moussa lagoon would rank as slightly polluted for, Cu, Zn, Cr and Ni.