Chemical structure, polymer microstructure, sequence distribution, and morphology of acid-bearing polymers are important factors in the design of polymer electrolyte membranes (PEMs) for fuel cells. The roles of ion aggregation and phase separation in vinylic- and aromatic-based polymers in proton conductivity and water transport are described. The formation, dimensions, and connectivity of ionic pathways are consistently found to play an important role in determining the physicochemical properties of PEMs. For polymers that possess low water content, phase separation and ionic channel formation significantly enhance the transport of water and protons. For membranes that contain a high content of water, phase separation is less influential. Continuity of ionic aggregates is influential on the diffusion of water and electroosmotic drag within a membrane. A balance of these properties must be considered in the design of the next generation of PEMs.