A comprehensive pore-scale modeling framework has been developed for the catalyst layer of a polymer electrolyte fuel cell in order to study the effects of site coverage and volume blockage owing to liquid water. The catalyst layer microstructure is reconstructed using a stochastic generation method. The liquid water distribution is obtained from a two-phase lattice Boltzmann simulation and the catalytic surface coverage leading to reduced electrochemical activity is estimated from the saturation maps. The pore blockage effect due to liquid water is evaluated using a direct numerical simulation model from the reduced oxygen diffusivity owing to the resistance offered by the blocked pores. copyright The Electrochemical Society.