Selective transport of specific ions across ion-exchange membranes can be enhanced by controlling membrane properties such as hydrophobicity. Previous studies have shown that hydrophobic membranes enhance transport of ions with low hydration energy, although such membranes often have increased electrical resistance. In the present work, we study the separation of monovalent ions, specifically nitrate and chloride, using newly-designed heterogeneous anion-exchange membranes. These membranes show high selectivity for nitrate over chloride and have low electrical resistance. We use a functionalized polymeric binder (ionomer) and three ion-exchange resins with different hydrophobic groups, i.e., resins with quaternary ammonium groups and methyl, ethyl, and propyl substituents, respectively. We find that in electrolyte solutions with nitrate and chloride, nitrate over chloride selectivity in our membranes increases with increasing length of the alkyl groups. The membrane with propyl groups, i.e., which has the highest selectivity for nitrate, was further tested in electrolyte solutions containing nitrate, chloride, sulfate, and nitrate, chloride, iodate. The transport of sulfate and iodate ions across the membrane with propyl groups was 6% and 2% of the total counterions transport, respectively. For monovalent ions with similar hydrated size it is possible to report selectivity trends based on the ion hydration energy. We find that the chemical structure of the membrane can either promote or hinder the transport of ionic species.