The removal of low molecular mass charged compounds from water streams in an ion exchange membrane bioreactor (IEMB) was studied. This integrated membrane process combines continuous ion exchange transport (Donnan dialysis) of the pollutant through a non-porous membrane, selective for the transport of mono-anions, and its simultaneous bioconversion to harmless products in a biocompartment. The mechanism of the process, governed by the Donnan equilibrium principles, allows for regulation of the direction and magnitude of flux of the individual anions present by adjusting the ratio of the impermeable co-ions between the biocompartment and polluted water compartment. Therefore, transport of a charged pollutant against its concentration gradient is possible. Experimental results, obtained for nitrate removal from drinking water are reported as a case study in order to evaluate the potential of the integrated process compared to that of other membrane-assisted bioprocesses as well as with Donnan dialysis operated as a single process. It was found that the IEMB process allows for the most selective removal of the target pollutant simultaneously avoiding microbial and secondary contamination of the treated water stream. The advantages, possible limitations and some recommendations for a successful IEMB process application are also briefly outlined.