A 3D lattice Boltzmann (LB) model with twenty-seven discrete velocities is presented and used for the simulation of three-dimensional porous media flows. Its accuracy in combination with the half-way bounce back boundary condition is assessed. Characteristic properties of the gas diffusion layers that are used in polymer electrolyte fuel cells can be determined with this model. Simulation in samples that have been obtained via X-ray tomographic microscopy, allows to estimate the values of permeability and relative effective diffusivity. Furthermore, the computational LB results are compared with the results of other numerical tools, as well as with experimental values.