In this work, a two-dimensional time-fractional subdiffusion model is developed to investigate the underlying transport phenomena evolving in a binary medium comprised of two sub-domains occupied by homogeneous material. We utilise an unstructured mesh control volume method to validate the model against a derived semi-analytical solution for a class of two-layered problems. This generalised transport model is then used to perform computational homogenisation on various two-dimensional heterogenous porous media. A key contribution of our work is to extend the classical homogenisation theory to accommodate the new framework and show that the effective diffusivity tensor can be computed once the cell problems reach steady state at the microscopic scale. We verify the theory for binary media via a series of well-known test problems and then investigate media having inclusions that exhibit a molecular relaxation (memory) effect. Finally, we apply the generalised transport model to estimate the bound water diffusivity tensor on cellular structures obtained from environmental scanning electron microscope (ESEM) images for Spruce wood and Australian hardwood. A highlight of our work is that the computed diffusivity for the heterogeneous media with molecular relaxation is quite different from the classical diffusion cases, being dominated at steady-state by the material with memory effects.