Abstract — Hydraulic fracturing techniques aim to create high conductivity channels through low permeability rocks, enhancing hydrocarbon flow to the wellbore. However, characterizing the reduction of mobility in fractures as a result of surface heterogeneities, has received limited attention. In this work, we study the effect of the heterogeneity in composition and roughness in flow through hydraulically induced fractures. Since analytical solutions are restricted to simple domains, a 3D direct simulation approach was selected. To assess these effects, domains exhibiting geometrical mineral arrangements, and self-affine fractures were created to carry out drainage and imbibition simulations. The relations of different wetting/non-wetting patterns and surface roughness, with interfacial areas, capillary pressure, and residual fluid saturation were quantified. We show that there is an effective mineral feature size related to the fracture dimensions that modifies the capillary pressure behavior. Similarly, the correlation range of the surface apertures determines the effect of the shape of a non-wetting front. Correspondingly, we found that for increasingly rough surfaces, there is a linear relation between the residual non-wetting saturation and capillary pressure with the aperture distribution. Thus, the shape, mineral size ratio, and surface roughness can have a significant effect on flow patterns. The results of this work can be used to improve macroscopic simulations, having a priori knowledge of the microscopic characteristics.