In the papermaking industry (reconstituted tobacco), a large number of tobacco stems, dust, and fines are discharged in the wastewater. This high salinity wastewater rich in ionic constituents and nicotine is difficult to be degraded by conventional biological treatment and is a serious threat that needs to be overcome. Electrodialysis (ED) has proved a feasible technique to remove the inorganic components in the papermaking wastewater. However, the fouling in ion exchange membranes causes deterioration of membranes, which causes a decrease in the flux and an increase in the electrical resistance of the membranes. In this study, the fouling potential of the membranes was analyzed by comparing the properties of the pristine and fouled ion exchange membranes. The physical and chemical properties of the ion exchange membranes were investigated in terms of electrical resistance, water content, and ion exchange capacity, as well as studied by infrared spectroscopy (IR) spectra, scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS) analyses. The results indicated that the membrane fouling is caused by two different mechanisms. For the anion exchange membranes, the fouling is mainly caused by the charged organic anions. For the cation exchange membrane, the fouling is caused by minerals such as Ca2+ and Mg2+. These metal ions reacted with OH− ions generated by water dissociation and precipitated on the membrane surface. The chemical cleaning with alkaline and acid could mitigate the fouling potential of the ion exchange membranes.