We present pore-scale simulations of two-phase flows in a reconstructed fibrous porous layer. The three-dimensional microstructure of the material, a fuel cell gas diffusion layer, is acquired via X-ray computed tomography and used as input for lattice Boltzmann simulations. We perform a quantitative analysis of the multiphase pore-scale dynamics, and we identify the dominant fluid structures governing mass transport. The results show the existence of three different regimes of transport: a fast inertial dynamics at short times, characterised by a compact uniform front, a viscous-capillary regime at intermediate times, where liquid is transported along a gradually increasing number of preferential flow paths of the size of one–two pores, and a third regime at longer times, where liquid, after having reached the outlet, is exclusively flowing along such flow paths and the two-phase fluid structures are stabilised. We observe that the fibrous layer presents significant variations in its microscopic morphology, which have an important effect on the pore invasion dynamics, and counteract the stabilising viscous force. Liquid transport is indeed affected by the presence of microstructure-induced capillary pressures acting adversely to the flow, leading to capillary fingering transport mechanism and unstable front displacement, even in the absence of hydrophobic treatments of the porous material. We propose a macroscopic model based on an effective contact angle that mimics the effects of the such a dynamic capillary pressure. Finally, we underline the significance of the results for the optimal design of face masks in an effort to mitigate the current COVID-19 pandemic.