The Oualidia lagoon provides important ecosystem services, such as fishing, aquaculture, tourism and high biological and ecological productivity. Many indices have been developed to evaluate environmental risks and to estimate the anthropogenic contribution of potentially toxic elements (PTE) in surficial sediments. The results show that the concentrations of the PTE found in surface sediments due to the anthropogenic activities in the area (urban effluents, aquaculture and agricultural areas) are significantly higher than those from the local background and sediment quality guidelines (SQGs). The potential ecological and biological risk index present satisfactory results. However, the sites near to the areas where anthropogenic activities are developed present 49% probability of toxicity, while the rest of the lagoon, present 9% to 21% probability of toxicity and low potential ecological risk, except for Hg where the risk was considered to be considerable. The PTE are mainly originated from the anthropogenic activities; nevertheless, anthropogenic contributions represent up to 69% of the total sediment of content, but it depends on the PTE: Cd (16%), Ni (38%), Zn (41%), Cr (43%), Cu (56%), Hg (68%), Pb (69%). Compared with the Sub-basin soils, the PTE are higher than 80%, hence the sub-basin feeds the lagoon by these elements (PTE).