Since 1994 the lagoon of Boughrara located in the south western coast of Tunisia was a seat of repeated episodes of harmful algal proliferation. Due to intoxications by shellfish harvested in this region the area was banned. In order to estimate the metal contribution to this phenomenon, seawater and bivalves collected from Boughrara during the algal bloom period were analysed for Cd, Cr, Hg, Pb, Cu and Al content using the atomic absorption spectrometry.The average of the metals and heavy metals concentrations in clams flesh and shells were lower or in the range of the European Union regularity limits and exhibited the following decreasing order: Al>Cu>Cd>Cr>Pb>Hg. Levels were ranging between 11.541 mg/kg and 0.025 mg/kg wet weights. For seawater and inter-shell water the order was approximately the same. The lagoon of Boughrara might be considered relatively unpolluted with metals and repeated toxic algal proliferations remained unexplained.