Natural organic matter (NOM) is thought to be a major source of fouling during membrane filtration of natural waters. The organic matter present in surface waters was characterized in terms of its molecular weight distribution, acidity and electrokinetic properties. The fouling potentials of anion exchange membranes were predicted by the characterization. Changes in the physicochemical properties of anion exchange membranes were also examined during electrodialysis (ED) process of solutions containing NOM. The ED performances were evaluated for the three anion exchange membranes (AMX, AM-1 and ACM) in the presence of NOM. Fouling phenomena in terms of current efficiency and NaCl flux were in good agreement with the fouling potentials predicted by the characterization results. Observations of the molecular weight distribution and the constituents of NOM revealed that the hydrophobic NOM fraction with high molecular weights deposited mainly on the membrane surface, providing fouling effects on the anion exchange membrane.