Contamination by polychlorinated biphenyls (PCBs) and hexachlorobenzene (HCB) was investigated along a spatial gradient in water, sediments and in commercially important bivalve species Scrobicularia plana, from Ria de Aveiro (Portugal). Organochlorines dissolved in water were below detection limit and concerning suspended particulate matter, only PCBs were quantified, ranging from 3.8 to 5.8 ng ∙ g−1 DW (Σ13PCBs). There was a distinct spatial gradient regarding PCB accumulation in sediments. The highest concentrations were found in deeper layers and closest to the pollution source, decreasing gradually along a 3 km area. Contamination in sediments exceeded the Canadian and Norwegian sediment quality guidelines, inducing potential toxic effects in related biota. PCBs tended to bioaccumulate throughout S. plana lifespan but with different annual rates along the spatial gradient. The maximum values were found in older individuals up to 3+ years old, reaching 19.4 ng ∙ g−1 DW. HCB concentrations were residual and no bioaccumulation pattern was evident. Congeners 138, 153 and 180 were the most accumulated due to their abundance and long-term persistence in the environment. In the inner area of the Laranjo Bay (0.6 km2), the species was able to remove up to 0.4 g of PCBs annually from sediments into their own tissues, which is consequently free for trophic transfer (biomagnification). Concerning human health, and despite the high concentrations found in sediments, PCB levels in bivalves do not exceed the limit established by the European Union for fishery products and are largely below tolerable daily intake. Although PCBs in Scrobicularia plana are present at low levels, their impact to human health after consumption over many years might be harmful and should be monitored in future studies. ; This research was supported by the FCT (Fundação para a Ciência e Tecnologia) through a PhD grant attributed to T.F. Grilo (SFRH/BD/ 44936/2008) and the MERCOAST project (PTDC/MAR/101906/2008), with funds from the POPH (Portuguese Operational Human Potential Program, the QREN Portugal (Portuguese National Strategic Reference Framework), and the MCTES (Portuguese Ministry of Science, Technology, and Higher Education). P. Pato acknowledges a postdoctoral fellowship from the FCT (SFRH/BPD/35068/2007).