Experimental determination of water permeability in unsaturated conditions is a critical issue. Among the existing experimental techniques, the instantaneous profile method is frequently used. When applied to bentonite-based materials, the method often shows that the water permeability–suction function significantly differs depending on the distance from the wetting face. Such behaviour has been interpreted as a consequence of structural changes in the sample which directly affect the water flow properties. In order to better understand the involved processes, a hydromechanical simulation of an infiltration test is performed. While structural changes are shown to affect the hydraulic properties, the computed water permeability–suction evolution is strongly affected by the interpretation of the raw experimental data.