The absorption efficiency (AE) of benzo[a]pyrene (BaP), a representative polycyclic aromatic hydrocarbon compound, in the green mussel Perna viridis was measured under different biological and food conditions (body size, food quantity, and food species). Uptake of BaP from the aqueous phase by different species of phytoplankton and green mussels was also experimentally quantified. A bioenergetic-based kinetic model was then used to separate the exposure pathways of BaP accumulation in the green mussels. Our results demonstrated that the AE of BaP in the green mussels ranged between 17 and 47%. Body size did not significantly affect the AE of BaP in the mussels. The AEs increased with a decrease in food availability, largely as a result of lengthening the gut passage of chemicals. The AEs differed by up to 2.3 times (17–39%) among the different food diets tested (four phytoplankton diets and one sediment diet). The BaP associated with the sediment was assimilated least efficiently. The difference in gut passage also appeared to account partially for the difference in AEs observed among different food types. No correlation between the AE and the distribution of BaP in the cytoplasm of phytoplankton cells was found. The concentration factor of BaP measured in four different marine phytoplankton species was in the range of 104 − 5 × 104 (L/kg). The calculated uptake rate constant of BaP in the green mussels was 6.37 L/g/d, and the efficiency of absorption of BaP from the aqueous phase was 6.6 to 8.8%. The model calculation indicated that under most circumstances, >56% of BaP in mussels can indeed be derived from the uptake from the aqueous phase. However, the relative importance of aqueous and dietary exposure can be affected by the variation of AE, mussel's ingestion rate, and concentration of BaP in ingested food particles.