The bioaccumulation of polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) was characterized in cockle, oyster and noble pen shell from nine areas in the Mar Menor lagoon with different hydrodynamic and pollutant sources. Biota, sediment and water samples were simultaneously collected in the spring and autumn of 2010. Considering all bivalve samples, PAH concentrations ranged from 8.98 to 370 mu g.kg(-1) d.w., those of PCBs from 0.15 to 42.36 mu g.kg(-1) d.w. and those of DDXs from below detection limit to 240.6 mu g.kg(-1) d.w., where p,p'-DDE was the main fraction. The bioaccumulation of PAHs was similar for cockle, oyster and noble pen shell, being higher close to ports and wastewater effluents. However, DDX and PCB bioaccumulations in oyster and noble pen shell were significantly higher than in cockle in spring (p = 0.02). The first organic pollutant bioaccumulation data for noble pen shell were obtained in this study, showing a preferential accumulation of pyrene. The increase of PAH bioaccumulation in autumn, as compared to spring, was low, due to high water temperatures during the summer, which favoured PAH dissipation processes. No significant seasonal variations were detected for OCPs and PCBs, except in some specific areas. The PAH, PCB and OCP levels detected in these bivalves were lower than OSPAR/MED POL environmental assessment criteria, except for p,p'-DDE in bivalves sited close to El Albujon watercourse mouth.