Bioavailability and bioaccumulation of polybrominated diphenylethers (PBDEs) are affected by adsorption on black carbon (BC) and metabolism in biota, respectively. Recent studies have addressed these two processes separately, illustrating their importance in assessing contaminant dynamics. In order to properly examine biomagnification of polychlorinated biphenyls (PCBs) and PBDEs in an estuarine food-web, here we set up a black carbon inclusive multichemical model. A dual domain sorption model, which accounted for sorption to organic matter (OM) and black carbon (BC), was used to estimate aqueous phase concentrations from the measured chemical concentrations in suspended solids. We adapted a previously published multichemical model that tracks the movement of a parent compound and its metabolites in each organism and within its food web. First, the model was calibrated for seven PCB congeners assuming negligible metabolism. Subsequently, PBDE biomagnification was modeled, including biotransformation and bioformation of PBDE congeners, keeping the other model parameters the same. The integrated model was capable of predicting trophic magnification factors (TMF) within error limits. PBDE metabolic half-lives ranged 21-415 days and agreed to literature data. The results showed importance of including BC as an adsorbing phase, and biotransformation and bioformation of PBDEs for a proper assessment of their dynamics in aquatic systems.