Typical proton-conducting polymer electrolyte membranes (PEM) for fuel cell applications consist of a perfluorinated polymeric backbone and side chains with SO3H groups. The latter dissociate upon sufficient water uptake into SO3 - groups on the chains and protons in the aqueous subphase, which percolates through the membrane. We report here systematic molecular dynamics simulations of proton transport through the aqueous subphase of wet PEMs. The simulations utilize a recently developed simplified version (Walbran, A.; Kornyshev, A. A. J. Chem. Phys. 2001, 114, 10039) of an empirical valence bond (EVB) model, which is designed to describe the structural diffusion during proton transfer in a multiproton environment. The polymer subphase is described as an excluded volume for water, in which pores of a fixed slab-shaped geometry are considered. We study the effects on proton mobility of the charge delocalization inside the SO3 - groups, of the headgroup density (PEM “equivalent weight”), and of the motion of headgroups and side chains. We analyze the correlation between the proton mobility and the degree of proton confinement in proton-carrying clusters near SO3 - parent groups. We have found and rationalized the following factors that facilitate the proton transfer: (i) charge delocalization within the SO3 - groups, (ii) fluctuational motions of the headgroups and side chains, and (iii) water content.