Understanding the gas migration in highly water saturated sedimentary rock formations is of great importance for safety of radioactive waste repositories which may use these host rocks as barrier. Recent experiments on drainage in argillite samples have demonstrated that they cannot be represented in terms of standard two-phase flow Darcy model. It has been suggested that gas flows along highly localized dilatant pathways. Due to very small pore size and the opacity of the material, it is not possible to observe this two-phase flow directly. In order to better understand the gas transport, a numerical coupled hydraulic-mechanical model at the pore scale is proposed. The model is formulated in terms of Smoothed Particle Hydrodynamics (SPH) and is applied to simulate drainage within a sample reconstructed from the Focused Ion Beam (FIB) images of Callovo-Oxfordian claystone. A damage model is incorporated to take into account the degradation of elastic solid properties due to local conditions, which may lead to formation of new pathways and thus to modifications of fluid transport. The influence of the damage model as well as the possible importance of rigid inclusions is demonstrated and discussed.