We have shown in our former study [1] that ordered microstructures can improve the effective electrical conductivity and permeability in the gas diffusion layer (GDL). However, the effect of ordered structures on the dynamics of gas-water dynamics in porous layers of fuel cells was not studied. Water management within fuel cell porous transport layers is a key challenge for improving performance. When liquid water accumulates at high current density, the oxygen diffusion resistance is increased. This study investigates the effect of GDL, microporous layer (MPL) and gas channel (GC) structure on the liquid water percolation and detachment in the channel. Dynamic two-phase flow simulations have been performed using OpenFOAM® with the Volume of Fluid (VoF) method to evaluate the water distribution in 2D and 3D ordered and disordered porous media. This study highlights the importance of pore morphology on improving the two-phase flow dynamics. The simulation approach was compared to x-ray micro computed tomography data of water injected into a GDL with detachment in the channel, which showed a high level of agreement. The effects of GDL pore morphology, defects in the MPL and interaction between GDL and GC on the water dynamics in the system have been studied.