Endosulfan (ES) is a micropollutant found in reverse osmosis concentrates from water reuse applications. Electrodialysis (ED) can remove and recover charged solutes from such concentrates. While polar compounds cannot normally be removed, their fate in ED is important as they can contribute to membrane fouling/poisoning and be released during cleaning. High adsorption of ES to ED membranes was observed. Consequently, the influence of solution pH and presence of humic acid (HA) on sorption mechanisms of ES to ion-exchange membranes during batch sorption isotherm and ED experiments were investigated systematically. ES-membrane partition coefficients (log KAEM/CEM) quantified through sorption isotherm experiments suggested that ES sorption was resultant of membrane catalysed ES degradation, hydrogen bonding and cation–π interactions between ES and membrane functional groups. ES sorption at pH 7 (550 μg/cm3) was greater than sorption at pH 11 (306 μg/cm3) due to alkaline hydrolysed ES and resultant decrease in bonding capacity with the membranes at high pH. The presence of HA reduced sorption at pH 7 (471 μg/cm3) and 11 (307 μg/cm3) due to HA competitive sorption. Partial membrane desorption was noted in isotherm (≤20%) desorption experiments and was dependent on the initial mass sorbed, solvent pH and resultant membrane interactions.