A novel method was used to estimate assimilation efficiencies (AEs) of dissolved and food associated PCBs (IUPAC 31, 49, and 153) by the Baltic Sea blue mussel (Mytilus edulis). Mussels were exposed to radiolabeled PCBs in a series of short-term toxicokinetic experiments at different algal food concentrations, both at apparent steady-state (ASS) and non-steady-state (NSS) conditions in respect to PCB partitioning between water and algae. The PCB AEs were calculated using a physiologically based bioaccumulation model where experimentally determined uptake and exposure rates at ASS and NSS conditions were combined into linear equation systems, which were solved for PCB AE from water and food. A positive relationship between PCB uptake and algae clearance by the mussels was observed for all three PCBs. The PCB AEs from both water and food increased with congener hydrophobicity (octanol/water partition coefficient [K(ow)]), but AEs decreased with increases in water pumping and filtration rate of the mussels, respectively, The average contribution of food-associated PCB to the total uptake also increased with K(ow) from approximately 30% for PCB 31 and PCB 49 to 50% for PCB 153, mainly as a consequence of increased sorption to the algal food.