Superficial and cored sediment samples from the Moulay Bousselham lagoon and sub-watershed were analyzed for Al, Fe, Cu, Zn, Pb, Mn, Ni, Cr, As, Hg, and Cd. The temporal and spatial distributions of the main contamination sources of heavy metals were identified and described using chemometric and geographic information system (GIS) methods. Sediments from coastal lagoons near urban and agricultural areas are commonly contaminated with heavy metals, and the concentrations found in surface sediments are significantly higher than those from 50-100 years ago. The concentrations of these elements decrease sharply with depth in the sediment column, and the elements are preferentially enriched in the <2-μm-sized fraction of the sediment. The zones of enhanced risk of heavy metals were detected by means of GIS-based geostatistical modeling. According to sediment pollution indices and statistical analysis, heavy metals (Pb, Cu, Ni, Zn, Cr, and Hg) that pose a risk have become largely enriched in the lagoon sediments during the recent period of agricultural intensification.