In this paper, direct-modeling-based Lattice Boltzmann Method (LBM) combined with in-situ flow visualization, is used to explore fundamentally the transport of liquid-water inside the gas-diffusion layers (GDLs) used in polymer electrolyte fuel cells. Studies of the water evolution, water saturation, and breakthrough pressure inside a GDL with single and multiple injection points under land and channel geometries are explored. The model and experiment demonstrate good agreement between geometries of GDLs provided in this study which were obtained by a three-dimensional (3-D), reconstructed micro-structure from micro X-ray computed tomography (CT). The overall predictions of water evolution within the GDL agree well with the data visualized from the X-ray CT experiment for all cases studied. It also reveals that the liquid-water saturation profiles inside the GDL and breakthrough pressure are different when the location of the water injection point is altered, thereby providing analysis as to the impact of microporous layers or catalyst-layer functioning. Moreover, the uncompressed GDL undergoes a significantly different mechanism of water transport than that of the compressed GDL. Furthermore, the predictions show that the wettability variation is one of the key factors of the saturation characteristics.