Density functional theory and classical molecular dynamics simulations permit us to elucidate details of ionic and molecular transport useful for the design of polymer electrolyte membranes. We consider two systems of current interest: (a) ionic transport in polyethylene-oxide compared to that in a polyphosphazene membrane targeted to be a good ionic carrier but a bad water carrier and (b) transport of oxygen and protons through hydrated nafion in the vicinity of a catalyst phase. It is shown that in polyphosphazene membranes, nitrogen atoms interact more strongly with lithium ions than ether oxygens do. As a result of the different complexation of Li+ with the polymer sites, Li+ has a much higher diffusion coefficient in polyphosphazene than in polyethylene oxide electrolyte membranes, with the consequent relevance to lithium–water battery technology. For the hydrated membrane/catalyst interface, our simulations show that the Nafion membrane used in low-temperature fuel cells interacts strongly with the catalytic metal nanoparticles directing the side chain towards the catalyst surface. Results at various degrees of hydration of the membrane illustrate the formation of water clusters surrounding the polymer hydrophilic sites, and reveal how the connectivity of these clusters may determine the transport mechanism of protons and molecular species.