In this work, a three-dimensional PEM fuel cell model has been developed and is used to investigate the effects of water flooding on cell performance parameters. The presence of liquid water in the cathode gas diffusion layer (GDL) limits the flow of reactants to the cathode catalyst layer, thereby reducing the overall reaction rate and curtailing the maximum power that can be derived from the cell. To characterize the effects of water flooding on gas diffusion, effective diffusivity models that account for the tortuosity and relative water saturation of the porous fuel cell electrodes have been derived from percolation theory and coupled with the CFD model within a single phase flow skeleton. The governing equations of the overall three-dimensional PEM fuel cell model, which are a representative of the coupled CFD and percolation theory based effective diffusivity models, are then solved using the finite volume method. Parametric studies have been conducted to characterize the effects of GDL permeability, inlet humidity and diffusivity of the reactants on the various cell performance parameters such as concentration of reactants/products and cell current densities. It is determined that the GDL permeability has little or no effect on the current densities due to the diffusion dominated nature of the gas flow. However, through the incorporation of percolation theory based effective diffusivity model; a marked reduction in the cell performance is observed which closely resembles published experimental observations. This is a reasonable approximation for effects of water flooding which has been inherently used for further parametric studies. (C) 2009 Published by Elsevier Ltd.