Models for pollution exposure assessment typically adopt an overly simplistic representation of geography, climate and biogeochemical processes. This strategy is unsatisfactory when high temporal resolution simulations for sub-regional spatial domains are performed, in which parameters defining scenarios can vary interdependently in space and time. This is, for example, the case when assessing the influence of biogeochemical processing on contaminant fate. Here we present INCA-Contaminants, the Integrated Catchments model for Contaminants; a new model that simultaneously and realistically solves mass balances of water, carbon, sediments and contaminants in the soil-stream-sediment system of catchments and their river networks as a function of climate, land use/management and contaminant properties. When forced with realistic climate and contaminant input data, the model was able to predict polychlorinated biphenyls (PCBs) concentrations in multiple segments of a river network in a complex landscape. We analyzed model output sensitivity to a number of hydro-biogeochemical parameters. The rate of soil organic matter mineralization was the most sensitive parameter controlling PCBs levels in river water, supporting the hypothesis that organic matter turnover rates will influence remobilization of previously deposited PCBs which had accumulated in soil organic matrix. The model was also used to project the long term fate of PCB 101 under two climate scenarios. Catchment diffuse run-off and riverine transport were the major pathways of contaminant re-mobilization. Simulations show that during the next decade the investigated boreal catchment will shift from being a net atmospheric PCB sink to a net source for air and water, with future climate perturbation having little influence on this trend. Our results highlight the importance of using credible hydro-biogeochemical simulations when modeling the fate of hydrophobic contaminants.