The hydro-mechanical properties of the vadose zone are strongly influenced by seasonal cycles. The hydraulic behavior of this zone is determined by the coupling of biotic and abiotic factors. The biotic factors are controlled by the physiology and anatomy of the vegetation growing in the area, while the abiotic factors depend on the local soil characteristics, such as water content, void ratio, and matrix structure. In this laboratory-scale investigation, we assess the influence of active biomass, water content, and suction on the particle and pore structure rearrangement. We use x-ray computed tomography and 3D digital image correlation to quantify plant roots at different stages of growth, soil deformation, and water content fluctuations. Our results show that the bulk porosity of vegetated soil is strongly affected by the induced water cycles. The global micro-structure rearrangement due to the double effects of plant water uptake and induced drying-wetting cycles translates into a final bulk porosity increase.