Several geotechnical structures constructed with fine soils submitted to wetting and drying (W-D) cycles face a variety of disorders. This is the case of some roads and slopes in the North of Tunisia where the upper soil layers are silty and clayey. Due to desiccation cracks, preferential pathways for rainfall infiltration and contaminant transport are created. In fact, the permeability varies significantly considering the evolution of desiccation cracks during W-D cycles. In the current research work, we developed an equipment of 150 × 150 × 50 mm, to measure the clay permeability during W-D cycles taking into consideration the influence of initial soil density. In addition, the role of the micro-structural evolution during the W-D cycles was investigated. The permeability was predicted using a proposed fractal model, based on the evaluation of the morphological parameters of cracks and the saturated permeability before crack development. The predicted and measured values of saturated hydraulic conductivity were found in good agreement. With cracking, the permeability can be increased to a limit value and the impact of the initial density becomes insignificant after seven W-D cycles.