The accurate estimation of hydraulic conductivity is important for many geotechnical engineering applications, as the presence of fluids affects all aspects of soil behaviour, including its strength. Darcy’s law is the key experimental (or phenomenological) equation employed to model ground water flow. Yet, this phenomenological equation can be linked to a more fundamental microscale model of flow through the pore spaces of the porous material. This paper provides an experimental verification of the relationships between Darcy’s law (macroscale) and the Navier–Stokes equations (microscale) for actual complex pore geometries of a granular material. The pore geometries are experimentally obtained through state-of-the-art X-ray computer assisted micro-tomography. From the numerical modelling of the microscale flow based on actual pore geometries, it is possible to quantify and visualize the development of pore-scale fluid preferential flow-paths through the porous material, and to assess the importance of pore connectivity in soil transport properties.