We investigated effective simultaneous removal of high loads of nitrate and perchlorate from synthetic groundwater using an ion exchange membrane bioreactor (IEMB). The aim of this research was to characterize both transport aspects and biodegradation mechanisms involved in the treatment process of high loads of the two anions. Biodegradation process was proven to be efficient with over 99% efficiency of both perchlorate and nitrate, regardless of their load. The maximum biodegradation rates were 18.3 (mmol m(-2) h(-1)) and 5.5 (mmol m(-2) h(-1)) for nitrate and perchlorate, respectively. The presence of a biofilm on the bio-side of the membrane only slightly increased the nitrate and perchlorate transmembrane flux as compared to the measured flux during a Donnan dialysis experiment where there is no biodegradation of perchlorate and nitrate in the bio-compartment. The nitrate flux in presence of a biofilm was 18.3 (+/- 1.9) (mmole m(-2) h(-1)), while without the biofilm, the flux was 16.9 (+/- 1.5) (mmole m(-2) h(-1)) for the same feed inlet nitrate concentration of 4 mM. The perchlorate transmembrane flux increased similarly by an average of 5%. Samples of membrane biofilm and suspended bacteria from the bio-reactor were analyzed for diversity and abundance of the perchlorate and nitrate reducing bacteria. Klebsiella oxytoca, known as a glycerol fermenter, accounted for 70% of the suspended bacteria. In contrast, perchlorate and nitrate reducing bacteria predominated in the biofilm present on the membrane. These results are consistent with our proposed two stage biodegradation mechanism where glycerol is first fermented in the suspended phase of the bio-reactor and the fermentation products drive perchlorate and nitrate bio-reduction in the biofilm attached to the membrane. These results suggest that the niche exclusion of microbial populations in between the reactor and membrane is controlled by the fluxes of the electron donors and acceptors. Such a mechanism has important implications for controlling the bio-reduction reaction in the IEMB when using glycerol as a carbon source and allowing treating a complex contamination of high concentrations of perchlorate and nitrating in groundwater and successfully biodegrading them to non-hazardous components. (C) 2016 Wiley Periodicals, Inc.