This study presents a comprehensive investigation on the water flooding of direct methanol fuel cells (DMFCs) during long-term testing with regard to the structural changes of the catalyst layer and gas diffusion layer (GDL) of the cathode. Two separate durability operations of DMFCs are conducted for 1000 and 1261 h in order to determine the relative contributions of the cathode catalyst layer and the GDL to time-dependent water flooding during the aging process. The voltage decay rates caused by flooding and non-flooding degradation phenomena are calculated and compared. DMFCs undergo serious voltage decay due to water accumulation in the cathode, and the rate of flooding degradation multiplies approximately every 500 h during the duration of testing. The cathode catalyst layer is found to be severely deformed due to surface wrinkling and cracking during the aging of the membrane electrode assembly (MEA). The morphological alteration of the cathode catalyst layer, particularly the formation of wide and deep cracks is identified as the main reason for the acceleration of water flooding, while degradation of the cathode GDL is minor. This demonstrates that during the long-term operation of DMFCs, the physical disintegration of the cathode catalyst layer is a crucial issue affecting water management, which should be carefully addressed. (C) 2014 Elsevier Ltd. All rights reserved.