Two critical parameters of nanophase morphology and water motion are discussed in the design of proton exchange membranes (PEMs). While much has been learned about the function of proton exchange membranes by studying poly(perfluorosulfonic acid) and sulfonated aromatic polymers, new generations of electrolytes for aqueous applications are being developed that push the limits of ion conductivity and small molecule transport rates in water-absorbing polymers. The utility of employing block copolymers has been demonstrated to concentrate and affect long-range connectivity of ionic domains, but the details of how ions arrange in these systems are still to be explored. Examples of block copolymer proton exchange membranes and their usefulness in understanding membrane function will be reviewed. Additionally, water motion in PEMs is critical to achieving sufficient proton conductivity. The relationship between water motion and conductivity can be used to design new materials with insight of the water-polymer interactions in the system.