Polybrominated diphenyl ethers (PBDEs) are a family where each congener possesses different physicochemical properties, persistence and/or toxicity. Biodegradation can selectively change the abundance of congeners. These warrant modeling of individual congeners by considering biodegradation pathways together with fate and transport (F&T) mechanisms. Accordingly, this study aims to develop a F&T model (Fate and Transport model for Hydrophobic Pollutants - FTHP) that integrates congener specific biodegradation of PBDEs in sediments. The model is tested using sediment data from a location representing the Lower South Bay of San Francisco. Results demonstrated settling, resuspension, and biodegradation as important mechanisms. FTHP is then used to predict congener concentrations in a period of 20 years for two cases (constant and time-dependent water column concentrations) and four alternative scenarios: no intervention (i.e., natural attenuation, also serves as the base case), no degradation, dredging and biostimulation. The greatest impact on the reduction of total PBDE concentrations was achieved by a reduction in water column concentrations, i.e. source control, and dredging. On the other hand, biostimulation coupled with source control was the most effective in reducing bioaccumulative PBDE congener concentrations and almost as effective as dredging for the rest of congeners. Proposed FTHP model can distinguish between congeners and help devise informed management plans which focus on decreasing risks associated with persistent and bioaccumulative compounds in contaminated sediments. (C) 2020 Elsevier Ltd. All rights reserved.