Surface sediments from Khnifiss lagoon (Morocco) were analyzed to evaluate the contamination degree of the area. Concentrations of V, Cr, Co, Ni, Cu, Zn, As, Cd, Hg, and Pb were determined on samples taken during the summer and the autumn of 2016. On the whole, higher concentrations were found in the summer season. The results revealed the following average concentrations (mg/kg), reported in descending order: Zn (51.7 ± 31.3) > V (38.8 ± 24.7) > Cr (26.6 ± 17.8) > Ni (16.5 ± 5.47) > As (8.50 ± 2.00) > Cu (6.60 ± 3.81) > Pb (6.13 ± 3.46) > Co (3.57 ± 2.09) > Cd (0.16 ± 0.11) > Hg (0.006 ± 0.001). Organic matter showed a positive significant correlation with some trace metals (mainly V, Cr, Co, Zn, Cd, Pb). Three pollution indices were calculated: Enrichment Factor (EF), Index of Geo−accumulation (Igeo), and Pollution Load Index (PLI). Minimal enrichments (for Zn, As, and Cd) were detected at some sampling points. Overall indices showed that the Khnifiss sediments can be classified as not contaminated, and that the trace metals amounts found are ascribable to the geogenic origin. The results of this work can be used as a starting point for further evaluations of trace metals distribution in Moroccan lagoons.