Abstract Consideration of the role of rock property variations is crucial in any analysis of the effects of deformation on fluid flow and mineralization. An empirical analysis of any mineralized terrain should consider this factor, in addition to those used in any other analysis of geometry and kinematics, such as orientation, evolution of the stress and strain fields, and the known distribution of veins, shear zones, breccias, and alteration. The conceptual models that arise from such an analysis can be enhanced by computer models. The models shown here are finite difference models that simulate fluid flow in deforming rock masses, one for fluid flow along predefined rock boundaries (Universal Distinct Element Code, UDEC), and another for fluid flow through deforming porous media (Fast Lagrangian Analysis of Continua, FLAC). UDEC modeling of the perturbed stress field around stronger, lower permeability meta-intrusive rocks in the Mary Kathleen district and the Hilton mine of the Mount Isa district, northwest Queensland, reproduces the observed location of the most intense veining and alteration. FLAC modeling of the Mary Kathleen U-REE orebody reproduces the location and geometry of ore shoots and provides an explanation for focusing of regional fluid towards the ore deposition sites. FLAC models of the giant Mount Isa copper deposit reveal that the effect of the rheological heterogeneity on fluid flow and solute transport is amplified if consideration is made of whether or not the rocks are contractant or dilatant, with increasing strain. Multiple working hypotheses can be evaluated quickly by such modeling; therefore, the models can be used in exploration and orebody extension studies. Furthermore, it is suggested from our work that the size and spacing of epigenetic, structurally controlled ore deposits is related in a fairly systematic way to the scale and degree of rock property variations, at least for a given strain history. For giant ore deposits to form, it requires that the gradients in pore pressure generated at local scales by heterogeneous rock packages must be subordinate to those operating at broader scales.