A polymer electrolyte fuel cell (PEFC) produces electrical energy thanks to the electrochemical reaction carried out inside the cell. During the energy conversion, water molecules are also produced in the cathode side and this can affect the diffusion parameters of the gas diffusion layers (GDLs). The generated water-drops due to the reaction may block the reactant gases and produce material oxidation. The mentioned phenomena influence the performance of the PEFCs. This paper aims to describe and quantify the impact on diffusion parameters of GDLs when the presence of formed water-drops inside the layer is considered. This study considers digitally generated GDLs, and the parameters considered are porosity, gas-phase tortuosity and diffusibility. The fluid flow behavior through the three-dimensional porous domain representing the GDL is obtained by using the lattice Boltzmann method (LBM). Depending on the water-drop size, the impact over the mentioned parameters can be computed. For the current study, a single water-drop has been placed into the GDL domain and its impact has been analyzed.