The solvation and transport of excess protons in polymer electrolyte membranes (PEM) such as NafionTM will be described using the multi-state empirical valence bond (MS-EVB) approach, combined with large scale molecular dynamics (MD) computer simulation. The MS-EVB method allows for the treatment of explicit (Grotthuss) proton shuttling and delocalization, which, in turn, strongly influences the properties of excess protons in various aqueous and otherwise complex environments. A significant extension of the methodology to treat highly acidic (low pH) environments such as the hydrophilic domains of PEM will also be presented. Results on proton solvation and transport in such environments will be presented which reveal the very significant role of Grotthuss shuttling in the acidic group proton dissociation process, as well as the subsequent excess proton solvation structures and transport properties.