The POPCYCLING-Baltic model, a nonsteady state spatially resolved mass balance model of chemical transport in the Baltic Sea environment was modified to include black carbon (BC), dissolved organic carbon (DOC) and food-web bioaccumulation. The importance of these modifications to the transport of PBDE congeners BDE-47, -99, -153, and -209 was assessed by comparing time-series simulated with and without black carbon and biota between 1970 and 2005. Inclusion of black carbon improved the model fit to measurements from air, soil, and biota, and had a major effect on the mass balance. Modeled bulk concentrations of PBDEs in sediments and soils increased by a factor of 3 while concentrations in biota decreased by a factor of 2-5. Black carbon also doubled the recovery time of the system due to the limited availability of PBDEs for degradation. In comparison, the inclusion of biota had only a minor effect on the overall mass balance and recovery times. The modified model is constructed as a flexible matrix and can also be applied to persistent organic pollutants in other ecosystems besides the Baltic Sea.