It is widely recognized that the performance degradation and the limiting current behavior in polymer electrolyte fuel cells (PEFC) are mainly attributed to the excessive build up of liquid water in the cathode side and the resulting flooding phenomena. Liquid water blocks the open pore space in the catalyst layer (CL) and the gas diffusion layer (GDL) leading to hindered oxygen transport and covers the electrochemically active sites in the CL thereby rendering reduced catalytic activity. The CL flooding therefore plays a crucial role in the overall PEFC performance limitation. In order to elucidate the primary mechanisms of liquid water removal out of the CL, the factors affecting CL flooding and to discern the role and contribution of CL flooding on the overall PEFC voltage loss, a CL flooding model has been developed. The flooding model is based on a simplified structure-wettability representation of the PEFC CL and a physical description of water and heat balance along with electrochemical performance analysis. The model shows that the evaporation mechanism, depending upon the cell operating temperature and the GDL thermal conductivity, plays a crucial role in the CL flooding behavior and the cell performance.