We argue that the observed conduit‐barrier behavior of fault zones in siliciclastic sedimentary aquifer systems can be understood by considering a strongly anisotropic hydraulic structure in the fault. Hydraulic anisotropy in the fault is expected from a variety of mechanisms including clay‐smearing, drag of sand, grain re‐orientation and vertical segmentation of the fault plane. In this paper, we present an algorithm to predict fault zone width, lithological heterogeneity and hydraulic anisotropy. Estimation of these parameters is based upon the amount of fault throw and the clay‐content of the lithologies flanking the fault zone. A suite of steady‐state flow models are presented using an idealized stratigraphy consisting of alternating clay and sand‐rich layers that are offset by a fault zone. These conceptual simulations show the impact of a fault zone on shallow (<500 m) fluid flow patterns and solute transport for different scenarios of fault throw. Fault width varies along the fault zone and increases from an average width of ~2 m for a throw of 50 m to ~8 m for a throw of 200 m. Hydraulic anisotropy in the fault zone in these scenarios is predicted to range between two to three orders of magnitude. Our results show that faults can form a preferential path way between aquifers at different depths over vertical distances of several hundreds of meters (that are otherwise separated by confining units) when fault permeability is strongly anisotropic. However, in the same scenario anomalously high hydraulic head gradients across the fault would still suggest that they act as an effective barrier to lateral groundwater flow. This has important implications for the assessment of the risk of a spread of contaminated groundwater or the reconstruction of hydrocarbon migration within sedimentary basins.