The bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) by the filter‐feeding soft‐shell clam Mya arenaria was evaluated at three sites near Boston (MA, USA) by assessing the chemical activities of those hydrophobic organic compounds (HOCs) in the sediment bed, water column, and organisms. Polyethylene samplers were deployed to measure the activities of HOCs in the water column. Sediment activities were assessed by normalizing concentrations with sediment‐water sorption coefficient values, including adsorption to black carbon in addition to absorption by organic carbon. Likewise, both lipids and proteins were considered in biota‐water partition coefficients used to estimate chemical activities in the animals. Chemical activities of PAHs in M. arenaria were substantially less than those of the corresponding bed sediments in which they lived. In contrast, chemical activities of PCBs in M. arenaria often were greater than or equal to activities in the corresponding bed sediments. Activities of PAHs, such those of pyrene, in the water column were undersaturated relative to the sediment. However, some PCBs, such as congener 52, had higher activities in the water column than in the sediment. Tissue activities of pyrene generally were in between the sediment and water column activities, whereas activity of PCB congener 52 was nearest to water column activities. These results suggest that attempts to estimate bioaccumulation by benthic organisms should include interactions with both the bed sediment and the water column.