Water management is an important issue in proton exchange membrane (PEM) fuel cell design and operation. The purpose of this work is to investigate the effects of the microstructure characteristics of the gas diffusion layer (GDL) and microporous layer (MPL), including pore size distribution, hydrophobic treatment, gas permeability, and other factors, on the water management and performance of a PEM fuel cell. A commercial catalyst-coated membrane with an active area of 25 cm2 is used along with a GDL and an MPL for assembling a single cell. The effects of the MPL, the thickness of the MPL, the PTFE loading of carbon paper and MPL, and the baking time of the MPL have been investigated. Results show that the addition of MPL increases cell performance in the high current density region due to the elimination of mass transfer limitation. There exists an optimum thickness of MPL. Furthermore, increasing the MPL baking time enhances cell performance due to enlarged pore size and permeability.