The Moulouya estuary located at the north-east of Morocco between 33° and 35° 30’north latitude and between 2° and 4°30’ west longitude receives the water from Moulouya River. This river can drain various pollutants from the backcountry who knows a strong agricultural activity marked by the massive use of fertilizers and pesticides. These pollutants might disturb the balance of the local marine environment. To measure the extent of this impact, the marine sediments in this area were analyzed to determine the content of heavy metals (Cd, Cu, Zn, Fe) in sediment fraction less than 63microns. We also studied the impact of sediment contamination on the small clam (Chamelea gallina) by the use of sequential extraction method of metal species. The results showed that the content of heavy metals (Cd, Cu, Zn, Fe) in sediments at both stations studied did not exceed the recommended guidelines from the U.S. National Oceanic and Atmospheric Administration levels (NOAA) and the Canadians on the Sediment Quality guidelines. The study of correlation between sediment contamination and that of bivalve showed the possible involvement of sediment contamination in the small clam by Cd, Cu and Fe. This correlation does not seem to be verified in the case of zinc. In order to better understand and assess the impact of sediment contamination on heavy metal levels recorded in the small clam, we expected to study the bioavailability of different metals by using different extraction methods sequentially. The results showed that although the contamination of sediment by iron, zinc and copper is sometimes marked, the forms present are mobilized only in certain percentage. So contrary to what can be concluded from the total digestion, sequential extraction suggests that the risk of this contamination on the small clam (Chamelea gallina) may be less noticeable.