This study presents the results of the systematic analysis of heavy metals in surficial sediments and marine molluscs from Oualidia and Sidi Moussa lagoons. The present field investigation determines baseline heavy metal conditions in two Atlantic lagoons for the purpose of prioritizing future lagoon remediation efforts. Heavy metal levels in the two lagoons were exceedingly high, but varied widely among sampling stations. PEC (probable effects concentrations) concentrations were often exceeded for heavy metals in the lagoon sediments, especially for Pb, Cd, As and Hg, and some stations had multiple metals at presumptively toxic levels. These comparisons suggest that sediment metal levels in the lagoons are clearly high and probably pose an environmental risk at some stations. Although a complete inventory of pollutant inputs has not been completed, major pollutant sources have been identified and they should be given first attention in remediation efforts. Therefore, a two-tiered remediation strategy is suggested: one tier aimed at source reduction by installing wastewater purification station at Oualidia lagoon and a second tier aimed at minimizing metal re-mobilization impacts, possibly via finer-sediment dredging, as water quality improves.