This paper proposes a stochastic model to simulate the occurrence and levels of polychlorinated biphenyls (PCBs) in juvenile tuna. This model can calculate the transport of PCBs in the ocean (macroscopic phenomena) and biomagnification in fish (microscopic phenomena). The uncertainty in the concentration of the PCBs encountered by fish was treated by adopting a random sampling from the probability distribution function using Metropolis–Hastings algorithm. The model was applied to one-dimensional cases with transported PCBs and swimming fish. The simulated PCBs levels in the fish agreed well with levels observed by previous studies. Influences of PCBs spatial distribution patterns and current velocity on the PCBs levels in fish body was examined. The results showed that the model was sensitive to the distribution pattern and moderately sensitive to the current velocity. The model has the potential to be extended to more realistic situations and to serve as a tool for environmental risk assessment. •This model can stochastically compute PCBs concentrations encountered by fish.•This models theoretically treated uncertainty in PCBs concentrations in seawater.•Dynamics of food chain and bioaccumulation was stochastically described.•The numerical calculations proved the adequate performance of this model.•Bioaccumulation of PCBs in fish was realistically simulated.