A numerical model of a proton exchange membrane fuel cell has been developed to predict the performance of a large active area fuel cell with the water cooling thermal management system. The model includes three submodels for water transport, electrochemical reaction, and heat transfer. By integrating those submodels, local electric resistance and overpotential depending on the water and temperature distribution can be predicted. In this study the effects of the inlet gas temperature and humidity on the fuel cell performance are explored, and the effect of the temperature distribution at different coolant temperatures is investigated. The results show that the changes in local electric resistance due to temperature distribution cause fuel cell power decrease. Therefore, the coolant temperature and flow rate should be controlled properly depending on the operating conditions in order to minimize the temperature distribution while maximizing the power output of the fuel cell.