While roots have been generally proved to be beneficial to soil mechanical behaviour, different and counterposed results have been found when investigating their effects on soil hydraulic response. Roots affect the hydro-mechanical and chemical properties of soils at different scales. In this regard, the paper focuses on studying the macroscopic hydraulic properties of root-permeated and compacted soils considering microstructural features coming from mercury intrusion porosimetry and X-ray micro-tomography. The results are interpreted bearing in mind the influence of the different soil hydraulic states on roots structure and physiology. The analysis of the results shows that roots growing in a compacted soil at low stresses are opening fissures while decreasing micropore volume inside aggregates due to chemical effects. This response has important effects on the hydraulic behaviour of the soil.