To examine the state of pollution of Bizerte Lagoon which is exposed to intense anthropogenic pressure, two sediment cores were taken at two sites, one undergoes the dual effects of both marine waters arriving from the Mediterranean Sea through the Channel, and also of freshwater from the Tinja River; the other core is located at the center of the lagoon where water depth is maximal (12 m). Heavy metal concentrations in the two cores were assessed, with calculated enrichment factors and geo-accumulation indexes. Core sediments were also studied for chemical speciation and their monosulfide contents were measured. Results from enrichment factors and geo-accumulation indexes show an accumulation of Cd, Zn, Cr, and Pb, while chemical speciation revealed a risk only from Cd and Mn. Comparison of sequential extraction values with those of acid volatile sulfides revealed that non-toxic effects may be caused by any of the studied metals in the sediment.