To achieve a cleaner production, textile wastewater with high organic and salt content can be treated by using Bipolar Membrane Electrodialysis (BMED) to minimize acid and base consumption in a dyeing process. While the dye molecules may foul the ion exchange membranes and strongly affect the desalination process. This work aimed to investigate the performance and fouling mechanisms of BMED during desalination of sodium sulfate from Remazol Brilliant Blue R (RBBR). Results showed that maintaining the zeta potential of RBBR above -25 mV may mitigate fouling of AEM during the BMED process. This confirms that, zeta potential of charged foulants (RBBR) plays a key role in terms of controlling membrane fouling. Accordingly, a new parameter "critical salt concentration" was introduced to control membrane fouling. Furthermore, energy dispersive X-ray spectroscopy (EDS), FT-IR and electrochemical analysis confirmed that fouling of anion exchange membrane by RBBR was due to electrostatic interaction. Finally, it was calculated that 72.02% of sodium and 66.9% of sulfate in the feed were converted to NaOH and H2SO4, respectively. This study proves that BMED process may be an alternative way treating textile wastewater with high salinity and the presence of dye molecules.