Abstract Long-term gas migration through clays cannot be simulated by conventional two-phase flow models alone owing to the presence of material deformation. In this article, an extended two-phase flow model that incorporates mechanical effects is proposed. The model allows the formation of preferential pathway and considers the relation between pore moisture and pore deformation. It was carried out with the intention of avoiding the complexity of a fully coupled thermal, hydraulic and mechanical modelling. In the new model, porosity, permeability, swelling pressure and pathways formation threshold depend on the water saturation. The model is validated on different gas injection experiments with controlled flow rate and controlled pressure. Some experiments are well known in the literature; some are new. In each case, an inverse approach is used to identify the model parameters. The results confirm that, depending on the type of bentonite (MX80, Avonlea, KunigelV1), modelling the gas migration could require the existence of a pressure-induced saturation-depending preferential pathway. In laboratory-scale experiments, the model leads to an accurate evaluation of the long-term gas migration trends, including not just the gas migration stage but also the water re-saturation level. In a field-scale experiment, the behaviour of the model in a realistic context is revealed.