The bioaccumulation and biomagnification of sediment-bound hydrophobic organic contaminants (HOCs) are of major concern for environmental and human health. In dynamic estuaries, HOCs can be taken up from sediments, porewater or overlying water column concentrations directly, or via the diet. The transfer of HOCs including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs) to resident/migratory biota was investigated in 11 finfish species and blue crabs (Callinectes sapidus) in the Passaic River estuary. Concurrently, passive samplers were deployed to assess porewater and overlying water column concentrations. Biota were assigned to three trophic levels based on their tissue 15N isotope values and published life history strategies. There were no significant differences in trophic magnification factors (TMFs) calculated based on life-history scenarios, implying that the migratory species, mostly juveniles, had equilibrated with in situ sources of pollutants at the time they were sampled. Bioaccumulation factors and TMFs were > 1 for most PCBs, tetra- and penta-CDD/DFs, indicating that they underwent biomagnification in the food web. All PAHs, PCB 11, and other lower chlorinated PCBs and PCDD/Fs did not magnify. Results from the analysis of HOC profiles implied that biota accumulated HOCs from sediments, porewater and diet, but not from overlying water.