Polymer electrolyte membrane (PEM) fuel cells have received increasing attention from both the public and fuel cell community due to their great potential for transport applications. The phenomenon of water flooding in the PEM fuel cells is not well understood, and few modelling studies have included the effect of water flooding. On the other hand, water management is one of the critical issues to be resolved in the design and operation of PEM fuel cells. in the present study, a mathematical model has been formulated for the performance and operation of a single polymer electrolyte membrane fuel cell. This model incorporates all the essential fundamental physical and electrochemical processes occurring in the membrane electrolyte, cathode catalyst layer, electrode backing and flow channel. A special feature of the model is that it includes the effect of variable degree of water flooding in the cathode catalyst layer and/or cathode electrode backing region on the cell performance. The model predictions have been compared with the existing experimental results available in the literature and excellent agreement has been demonstrated between the model results and the measured data for the cell polarisation curves. Hence, this model can be used for the optimisation of PEM fuel cell design and operation, and can serve as a building block for the modelling and understanding of PEM fuel cell stacks and systems.