Knowing the movement of water in polymer electrolyte fuel cells (PEFCs) is important for deciding the optimum shape of the cell and the optimum operating conditions. It is well known that PEFCs show the best performance under conditions of moderate relative humidity. However, the experimental measurement of water movement is difficult because of the flow through the complex geometry of the diffusion layer. Therefore, to observe the movement of water in a PEFC, microscopic analysis was performed by the lattice gas automata (LGA) method. The influence of prevention of gas diffusion by water was investigated. According to the channel configuration, the distribution of water was observed in the diffusion layer and the distribution of the extent of reaction between oxygen and hydrogen was affected. Moreover, because the influence of prevention of gas diffusion by water on the cathode side was more pronounced than that by water on the anode side, it was determined that the cathode side affects cell performance markedly.