In this study, the effect of location, wettability, and thickness of the hydrophilic layer and also the effect of microporous layer (MPL) thickness on the dynamic water transport in the gas diffusion layer (GDL) of polymer electrolyte membrane fuel cell (PEMFC) is investigated using the Lattice Boltzmann method. The effect of the presence of hydrophilic layer and MPL on the number of dominant flow paths, liquid water breakthrough sites, liquid water loops, liquid water pools, and time required to reach steady-state for 12 cases have been investigated. Results showed that if the hydrophilic layer is near the MPL/GDL interface, flooding will occur. Also, comparing with purely hydrophobic GDL, reduction of hydrophilic layer thickness in the GDL/GC interface reduces the water saturation level by 11.8% and the time required to reach steady-state by 8.88%. Moreover, this study indicated that adding a thin layer of MPL at the catalyst layer (CL)/GDL interface with present a hydrophilic thin layer at the GDL/gas channel (GC) interface reduces the liquid water saturation level by 50.1% and the steady-state time by 38.9%. Furthermore, the details of the dynamic behavior of water in the GDL under different hydrophilic conditions have been reported and discussed.