Nafion, the most widely used polymer for electrolyte membranes (PEM) in fuel cells, consists of fluorocarbon backbones and acidic groups that, upon hydration, swell to form percolated channels through which water and ions diffuse. While the effects of the channel structures and the acidic groups on water/ion transport have been studied before, the surface chemistry or the spatially heterogeneous diffusivity across water channels has never been shown to directly influence water/ion transport. Using molecular spin probes that selectively partition into heterogeneous regions of PEM and Overhauser dynamic nuclear polarization relaxometry, this study reveals that both water and proton diffusivity are significantly faster near the fluorocarbon and the acidic groups lining the water channels compared to within the water channels. The concept that surface chemistry at the (sub-)nanometer scale dictates water and proton diffusivity invokes a new design principle for PEM.