A methodology to assess the effects of structural heterogeneities below seismic resolution in porous carbonate grainstones on reservoir performance during production is developed by integrating structural analysis, power law distributions, up-scaling, and numerical techniques. The novelty of the methodology consists in accounting for the buffering effects on permeability caused by compactive and cataclastic deformation bands. By using this methodology, a 3D deterministic field analogue and a 3D Discrete Fracture Network (DFN) representations of the reservoir/aquifer were built first, and then single-phase, steady state fluid flow numerical experiments in an equivalent porous medium framework were performed. The field analogue is located along the North-western coast of Sicily (Italy) where Lower-Pleistocene porous carbonate grainstones are cross-cut by a strike-slip fault system. This fault system is made up of two conjugate sets of strike-slip shear structures recognized as single compactive shear bands (CSB), zones of compactive shear bands (ZB) and well-developed faults (DF), with discrete slip surfaces and cataclastic material. The permeability of these structures is up to three orders of magnitude less than the surrounding porous carbonate rocks. The fluid flow numerical experiments have been performed on the two aforementioned reservoir/aquifer descriptions to assess the effect of Sub-Seismic Resolutions Faults (SSRF), such as those observed in the outcrops, on fluid flow during production from a well, injection-production in Enhanced Oil Recovery (EOR), and up-scaling to large cell size for regional flow simulation. Comparison of draw-down modelling in the DFN and the deterministic models show that results are similar with the exception of wells located in areas of intense strain localization with ZB and DF. The use of the DFN model is therefore an acceptable representation of the heterogeneities induced by SSRF in a reservoir/aquifer. Results of numerical computations show that, in structurally complex areas, SSRF-related ZB and DF might represent a drilling risk because they can enhance draw-down during production and EOR activities.