The removal of the trace inorganic contaminants boron (B(OH)4−), fluoride (F−) and nitrate (NO3−) from synthetic aqueous solutions containing organic matter using electrodialysis was investigated. The transport of the contaminants through the ion-exchange membranes was evaluated in relation to hydrated ionic radius, whereby a positive correlation was found in absence of organic matter. NO3−, with the smaller hydrated ionic radius and weaker hydration shell, was removed more effectively than F−, which has a larger hydrated ionic radius and stronger hydration shell. The removal of F− and NO3− was not significantly influenced by solution pH due to their pH independent speciation. However, the removal of boron was dependent on increasing solution pH and the degree of demineralization. Dissolved organic matter (humic acid, tannic acid and alginic acid) resulted in enhanced removal of boron and F− as a result of the binding of F− within the organic matter structure and complexation of boric acid (B(OH)3) with carboxylate groups in the organic matter. Deposition of organic matter to the anion-exchange membranes was noted. Inorganic trace contaminant and organic matter membrane deposition influenced system performance in regards to an increase in stack resistance and decrease in removal and flux of total dissolved solids.