The Moroccan Southern Atlantic coast is mainly influenced by upwelling, Saharan dust and anthropogenic micropollutant input. These factors contribute to increasing the availability of metal elements in waters. To differentiate human impact from natural variability, knowledge of background concentrations of metals and their fluctuations in bioindicator organisms such as zooplankton is important. This work aims to determine the levels of metals elements (Zn, Mn, Pb, Cu, Cd, Cr, Co, Ni, Li, As, Sr, U, Fe and Ba) in zooplankton along the southern area of the Atlantic coast of Morocco. Zooplankton samples were collected in the summer (July 2013) and autumn (December 2013) at 27 stations from Sidi Ifni to the south of Dakhla. All stations were located on transects perpendicular to the coast. The analysis of metal elements in zooplankton was determined by ICP–MS. The results revealed that in all transects, metal concentrations were below the regulatory limits. Metal enrichments were observed in the south and decreased gradually to the north. This study can be used as baseline data for the metal contents of zooplankton in Moroccan South Atlantic coastal water. A comparison to worldwide reported data on zooplankton did not reveal any suggestions on increased metal presence in the area investigated.