We have applied reactive transport simulations to evaluate conceptual models of hydrothermal fluid flow related to the Mesoproterozoic Mount Isa copper mineralisation. Numerical experiments have been performed specifically to investigate whether fluid flow was driven by mechanical deformation, higher than hydrostatic fluid pressure gradients, or thermal buoyancy, and what the mechanism of ore deposition was. One distinct feature of the Mount Isa mineralising system is a region of massive silica-rich alteration that surrounds the copper ore bodies within the Urquhart shale, indicating upward flow of a cooling fluid. Hydromechanical modelling revealed that contraction and horizontal shear can produce a dilation pattern that favours upward fluid flow, whereas strike slip movement causes dilation of pre-existing vertical structures. Reactive transport models show that hydraulic head driven flow is more likely to produce a more realistic silica alteration pattern than free thermal convection, but neither process generates a flow pattern capable of precipitating copper at the appropriate location. Instead we propose that gravity driven flow of a dense oxidised basin brine led to chalcopyrite mineralisation by fluid-rock reaction.