Rock deformation has an important effect on the spatial distribution and temporal evolution of permeability in the Earth's crust. Hydromechanical coupling is of fundamental significance to natural fluid–rock interaction in porous and fractured hydrothermal systems, and in the assessment and production of hydrocarbon resources and geothermal energy. Shearing and fracturing of rocks can lead to the creation or destruction of permeability when fractures or faults form, or when existing structures are reactivated. Changes in stress orientation or fluid pressure can drive rock failure and create dilating fault zones that have the potential to focus fluid flow, or to breach seals above overpressured fluid compartments. Here, numerical models of deformation and fluid flow related to Mesoproterozoic copper mineralisation at Mount Isa, Australia, are presented that show how changes in deformation geometry in multiply deformed geological architectures relate to changes in dilation patterns, fluid pathways and flow geometry. Coupled numerical simulations of deformation and fluid flow can be useful tools to better understand structural control on fluid flow in hydrothermal mineral systems.