A comprehensive pore transport model is proposed to describe proton diffusion within Nafion at various hydration levels by incorporating effects of water uptake and various proton transport mechanisms, namely, proton hopping along surface, Grotthuss diffusion, and ordinary mass diffusion of hydronium ions. The diffusion coefficients are predicted within a general random walk framework. The proton conductivity in contact with water vapor is accurately predicted as a function of relative humidity without any fitted parameters, considering the sorption isotherm proposed in the companion paper (Part 1). A maximum conductivity in contact with liquid water is also predicted by the model for equivalent weight between 900 and 1000, in good agreement with the experimental measurements. The modeling framework could be extended to other proton conducting electrolytes for fuel cell applications. (c) 2005 The Electrochemical Society.