Three-dimensional, multicomponent and multiphase transport computations are performed using a computational fluid dynamics (CFD) code (FLUENT) with a polymer electrolyte membrane (PEM) fuel cell module, which has been further improved by taking into account the detailed composition and structure of the catalyst layers using a multiple thin-film agglomerate model. In this model, reactant concentrations are dependent on transport through liquid water (caused by flooding in the catalyst layer) and polymer electrolyte films which surround the catalyst sites. The results of CFD computations show that transport limitations associated with the liquid water and polymer electrolyte have substantial negative effects on PEM fuel cell performance.