The ionic conductivity of polymer electrolyte membranes (PEMs) is an essential parameter for their device applications. In water-swollen PEMs, protons and other ions are transferred through hydrophilic channels of a few nanometers in diameter at most. Thus, optimizing the chemical and physical properties of the channels can enhance the conductivity of PEMs. However, the factors controlling the conductivity have not been completely clarified. Here, we report that measurements taken near the channel walls by a special nuclear magnetic resonance technique with ≤1 nm spatial resolution showed the largest water diffusivity when ∼80% of hydrophilic sulfonic acid groups were blocked, but the proton conductivity was low. The water diffusivity was much less affected by differences in water content. Our results provide a concept for changing the properties of PEMs and a challenge to implement the improved diffusivity in a way that enhances net ion conductivity.