An integrated approach, involving land use patterns and heavy metal contents of the surficial and cored sediment, was proposed to detect the characteristic spatial and temporal scale of point and non-point source human disturbances on the Oualidia lagoon in Morocco. Identification and description of the temporal and spatial distributions of the main contamination sources of heavy metals are analyzed using statistics and GIS methods. The results show that surficial sediments are highly enriched in heavy metals compared to their preindustrial background levels. Land-use types affected lagoon sediment pollution in different ways: 1) Agricultural areas had the highest potential for sediment contamination by heavy metals, particularly Pb, Cu and Hg, 2) Ni and Cr are the main pollutants originating from urban sewage and 3) oyster farming and traditional land uses such as salt flats, pastures showed low levels of others metals. The enrichment factors (normalized by Al) obtained from the sediment cores indicated that the lagoon is (strongly/moderately) polluted by all metals which were attributed to agricultural activities and wastewater discharges from urbanized areas.