Since low permeability rock has the potential to behave as an actual semi-permeable osmotic membrane, chemical osmosis may have an effect on water flow and needs to be accounted for in analysis. Hence, an advanced fully coupled formulation for modelling unsaturated hydro, chemical and mechanical effects is here presented based on modified mixture theory. Firstly, the classical Darcy’s law has been modified to include the chemical potential. Secondly, the mechanical deformation, which affects the permeability, has been coupled with the water and chemical flows by using Helmholtz free energy and the Gibbs–Duhem equation. Finally, an illustrative numerical example with relevance to radioactive waste disposal has been analysed to investigate the performance of the coupled formulation and the relative influence of parameters.