Sedimentary basins and underlying basement rocks constitute significant reservoirs for the extraction of groundwater, hydrocarbons, and geothermal resources, and the disposal of waste fluids including captured anthropogenic CO₂ and radioactive waste. The migration of these fluids under natural and engineered conditions is influenced by structural discontinuities that include faults, fractures, dissolution surfaces, and deformation bands. Understanding the coupled mechanical and chemical processes that control the hydromechanical evolution of these structures is of applied significance for resource development, energy production, earthquake hazard assessment, and natural habitat preservation. Significant recent advances have been made in the field of faults, fractures, and fluid flow in sedimentary basins. The most prominent are (1) the occurrence of seismicity in areas of historically low seismic activity attributed to oil and gas extraction, (2) the recognition of slow seismic events and advances in the understanding of weak faults, (3) advances in radiometric dating of structural processes and paleo-fluid flow, (4) improved understanding of coupled chemical and mechanical processes in rock failure under upper crustal conditions, (5) imaging of fluid flow and deformation processes using active and passive geophysical techniques, (6) the discovery of extremely high-temperature gradients associated with hydrothermal flow through fault zones, and (7) significant advances in numerical simulations from the pore to the basin scale. The aim of this special issue is to highlight recent research into these and related topics to provide an updated state-of-the-art assessment of the role of faults and fractures in controlling local- and regional-scale fluid transport in sedimentary basins and subjacent basement rocks. The special issue welcomes multidisciplinary contributions that exhibit the full breadth of structural controls on fluid flow and potential feedback mechanisms, encompassing research focused on a diverse range of lithologies and tectonic settings, with an equal balance of academic significance for fluid–rock interaction and their implications for industrial and environmental applications.