Synthetic polymer membranes are enabling components in key technologies at the water–energy nexus, including desalination and energy conversion, because of their high water/salt selectivity or ionic conductivity. However, many applications at the water–energy nexus require ion selectivity, or separation of specific ionic species from other similar species. Here, the ion selectivity of conventional polymeric membrane materials is assessed and recent progress in enhancing selective transport via tailored free volume elements and ion–membrane interactions is described. In view of the limitations of polymeric membranes, three material classes—porous crystalline materials, 2D materials, and discrete biomimetic channels—are highlighted as possible candidates for ion-selective membranes owing to their molecular-level control over physical and chemical properties. Lastly, research directions and critical challenges for developing bioinspired membranes with molecular recognition are provided.