The present study focuses on investigating the effects of biological compartment conditions on the transport of nitrate and perchlorate in an Ion Exchange Membrane Bioreactor (IEMB). In this hybrid process, the transport depends not only on the membrane properties but also on the biological compartment conditions. The experiments were planned according to the Plackett-Burman statistical design in order to cover a broader range of experimental conditions, under which a previously developed mechanistic transport model was not able to predict correctly the transport fluxes of the target pollutants. Using Principal Component Analysis, it was possible to identify not only the concentrations of target (nitrate and perchlorate) and of major driving counter-ion (chloride) but also those of some biomedium components (e.g. ammonia, ethanol and sulphate) as variables that affect the transport rate of micropollutants across the membrane. These conclusions are based on the loadings of the two first principal components that describe 84% of the data variance. The present study also revealed that the hydraulic retention time and the hydrodynamic conditions in the biocompartment have a minor contribution to the micropollutants transport. The results obtained are important for process optimization purposes.