Abstract Shale rock is challenging to characterize due to its complex multiscale structure, which directly influences various mass transport processes. The diffusion of a single component fluid through shale rocks is further complicated by the existence of various pore types, e.g. organic or intercrystalline, and fractures that range in size from sub-nanometer to micrometer. We present a workflow that investigates the process of liquid/liquid diffusion in shale rocks, which provides insights into its multiscale structure. We combine scanning electron microscopy (SEM), focused ion beam-scanning electron microscopy (FIB-SEM), pore-scale simulations and high-resolution 4D X-ray microcomputed tomography to investigate shale structure and effective diffusivities at various length scales. We find that fractures, matrix heterogeneity and pore-level characteristics are important factors that influence mass transport. Fractures influence effective diffusivities at the core scale providing high diffusivities over early time scales. Matrix heterogeneity results in effective diffusivity differences at the sub-core scale that are lower than the effective diffusivities measured at the core scale at early time. Effective diffusivities for organic matter rich regions are at least one order of magnitude greater than regions with low organic matter. Within the organic matter rich regions, effective diffusivities are mostly within one order of magnitude. These analyses provide a framework to build multi-scale shale models based on the pore-scale structure (10−9 m) of organic matter rich regions, distribution of porosities at the sub-core scale (10−6 m) and the arrangement of fractures at the core scale (10−3 m).