In this work, a three-dimensional multiphase non-isothermal model incorporated with a capillary-extended sub-model in gas channels is used to investigate the coupled phenomena of water and thermal transport in proton exchange membrane fuel cells. Distributions of water and temperature along the flow path in the channel are highlighted and the pros and cons of various operating temperatures are elaborated. In addition, this work also sheds light on the impacts of temperature variations of bipolar plates induced by non-uniform cooling conditions, which have been overlooked by most previous works. An important phenomenon of water distribution, dry-out at inlets and flooding at outlets (DIFO), is observed and this non-uniform distribution is revealed to be greatly influenced by the operating temperature, inlet relative humidity and gas flow stoichiometry. Moreover, temperature variations of bipolar plates are shown to exert remarkable impacts on water distribution. Consequently, optimum matching between water and temperature fields is proposed to be of vital importance in fuel cell design, e.g., strong cooling at the inlet and weak cooling at the outlet are demonstrated to be a feasible way of mitigating the problem of DIFO. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.