The effect of thickness and wetproof level of the gas diffusion layer on electrode flooding and cell performance was investigated. Three types of gas diffusion media were tested: SGL SIGRACET carbon papers, with and without a microporous layer, and Toray TGPH carbon paper without a microporous layer. Overall, it was found that SGL carbon paper with the microporous layer gave the best fuel cell performance even at low air stoichiometries. It was also found that adding poly (tetrafluoroethylene)(PTFE) to the gas diffusion layer could enhance gas transport and water transport when a cell operates under flooding condition, but excessive PTFE loading could lead to a high flooding level in the catalyst layer. It is our opinion that a combination of hydrophobic pores for gas transport and hydrophilic pores for liquid water transport within the macroporous layer is needed. It is also our opinion that the optimal ratio of hydrophobic and hydrophilic pores depends on the pore size and its distribution. Finally, it was observed that without the microporous layer, thinner gas diffusion materials were more sensitive to liquid water accumulation than the thicker ones.