The partitioning of PCBs to natural populations of aquatic heterotrophic bacteria from Lake Superior was measured in both field and laboratory studies to better understand the role of bacteria and the microbial food web in persistent, bioaccumulative, toxic organic contaminant (PBT) transfer. A filtration method that separated material > 1 μm from that < 1 μm was used to collect and measure PCB concentrations in the bacterial fraction. We used bacterial biovolume and a conversion factor to calculate bacterial carbon, which was used to normalize PCB concentrations. The range of total PCB concentrations in the bacterial fraction (61-337 ng/g organic carbon; OC) was similar, but generally higher than that of the total particulate fraction (36-324 ng/g OC). Measured log bioaccumulation factors (BAFOC, bacterial fraction; KOC, total particulate) were significantly greater in the bacterial fraction than in the total particulate fraction (bacterial range 6.7-7.3, total particulate range 5.8-7.0). Laboratory experiments demonstrated that a hexachlorobiphenyl reached steady state with a natural community of Lake Superior bacteria within 48 h and had a mean log BAFOC of 7.5 ± 1.9. The octanol/water partition coefficient (KOW) consistently underpredicted BAFOC, however, the magnitude of the underprediction was still within the range of uncertainty in food web modeling (factors of 3-9). Food web modeling and risk assessment of PBT bioaccumulation in aquatic systems could be improved by considering the microbial food web (bacteria and its protozoan grazers) as a previously unaccounted for pathway of contaminant transfer.