Pentabromodiphenyl ether is one of the most abundant flame retardant additives detected in treated municipal wastewater, river water and sediments in China. When using treated municipal wastewater for recharging river-based natural groundwater, polybrominated diphenyl ether (PBDE) pollution might be a potential threat to underground aquifers. Lab-scale column experiments simulating recharge were conducted to investigate the migration and biodegradation of 2,2',4,4'5-pentabromodiphenylether (BDE-99) under different recharge modes. Three recharge columns were operated in continual sterilization recharge (CSR), continual recharge (CR), and wetting and drying alternative recharge (WDAR). The results showed that the attenuation effect of the BDE-99 was in the order of CR>WDAR>CSR, whereas the intermediate products of PBDE biodegradation were in the order of WDAR>CR>CSR. The attenuation rate constants of BED-99 in the CSR, CR and WDAR systems were 0.105, 0.139 and 0.127 m(-1), respectively, which followed first-order kinetics. The primary debrominated metabolites were BDE-15,-28,-47 in the CR system, whereas high-brominated diphenyl ethers (BDE-153,-154,-183) and isomers of BDE-99 (BDE-100) were also produced during the biotransformation process in the WDAR system. The accumulation amount of BDE-99 was higher in WDAR soils than in the CR system, whereas the intermediate product concentration of PBDEs and OH-PBDEs were in reverse order. According to the high-throughput sequencing, the bacterial community in the upper layer was more diverse than in the bottom layer, which was related to the oxygen concentrations, BDE-99 and its halogenated intermediate concentrations in the water-soil system. The dominant groups were found to be proteobacteria, Acidobateria, and Firmcutes, including Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Acidobateria-6, and Clostridia, suggesting that these microbes might play an important role in BDE-99 and intermediate metabolite degradation. The findings of this study provide an understanding of PBDE accumulation in natural groundwater recharge areas under different recharging operation modes and can facilitate the prediction of the fate of PBDEs in underground aquifers. (C) 2016 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.