Understanding the mechanisms of large-scale, subsurface hydrogen migration is essential for natural hydrogen exploration and for hydrogen storage assessment. The unique properties of hydrogen make the timescales of hydrogen migration within geological basins vary from thousands of years to days. Within the shallow Earth, diffusive and advective transport mechanisms are dependent on a wide range of parameters, including geological structure, microbial activity and subsurface environmental factors (e.g. salinity, temperature and pressure). In this study, we review the nature and timescale of hydrogen migration in geological basins. We also review the mechanisms and timescales of hydrogen migration within diffusive, advective and biologically moderated systems within the shallow Earth. We calculate maximum vertical velocity for several key rock types, including sandstone and micrite, and discuss the importance of capillary pressure in controlling the mode of hydrogen migration in sedimentary rocks. Finally, we discuss the potential application of causal analyses methods to constrain complex processes in hydrogen systems and assess the challenges of conventional reservoir modelling for hydrogen migration.