Literature studies are evidencing the counterposed effects of vegetation on soil hydraulic behaviour. Besides, root effects at the microscale are rarely quantified for direct correlations with phenomenological observations due to the complexity of adopting up-scaling factors. This study explores the microstructural causes behind the observed changes in vegetated compacted clayey sand's hydraulic and volume change behaviour. To this aim, laboratory experiments were carried out on compacted samples seeded with Cynodon dactylon. Significant changes in soil water-saturated permeability, water retention and shrinkage upon drying were observed after root growth. Laboratory measurements were complemented with quantification of root morphological features and observations at the microscale at different soil hydraulic states. X-ray scans and mercury intrusion porosimetry allowed covering seven orders of magnitude of pore sizes, shedding light on soil fabric changes at the soil-root interface and the clay aggregate scale. The effects of roots on the soil pore size distribution consisted of multi-physics phenomena: fissure generation, void clogging, and soil aggregation due to roots’ chemical interaction. Furthermore, a good correlation was found between the normalised volume of roots and the micro-pores volume. This new expression was included in a framework to predict soil water retention behaviour considering the aggregated structure and soil-root hydro-chemical interactions.