A three dimensional two phase flow model is proposed to study transport phenomena in a PEMFC. In order to capture the effects of liquid water on the performance of the fuel cell, all regions are modeled from the anode to the cathode as having finite thickness. The geometry of the bipolar plate is modeled in detail to capture the effect of liquid water accumulation under the channel rib. This model takes into account the effect of temperature and inlet RH of both the anode and cathode. The three-dimensional model uses the finite volume method to solve the equations of mass conservation, momentum, energy, species transfer and protonic potential. These equations include the effect of liquid water on the transport properties as well as the electrochemical source. The effects of water on ohmic losses are presented for different humidity conditions of the anode and cathode at various fuel cell temperatures. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.