The X-ray microtomography technique allows discrimination of air, water, roots, mineral and organic particles based on differences in the respective linear attenuation coefficients as well as the image spatial resolution and particle, pore and root size distribution, which define the contrast among the soil phases. In general, benchtop, medical and pre-clinical microCT systems operate at relatively low energy and polychromatic X-ray spectra which allow good differentiation between the highly contrasting solid and air phases, but provide low contrast when roots, water and air-filled space should be differentiated. To enhance contrast of this multiphase, dynamic and very complex system some strategies can be applied, e.g. the use of metallic filters to reduce soft X-rays (“Bremsstrahlung”), the addition of dopants as iodine to the soil solution and increasing the spatial resolution of the image acquisition. In this work we test these strategies for enhancing contrast and improving discrimination of roots, water, air-filled pores and mineral particles, using a benchtop microCT scanner. Undisturbed samples of two oxisols with contrasting texture (a very clayey and a sandy one) were collected in plastic rings of two diameters (40 and 20 mm). The samples were irrigated with water or with a 1% potassium iodine solution. One corn seed was sown per ring. Ten days after germination, rings were imaged with or without an aluminum/copper filter. All samples were then submitted to water stress during 3 days and imaged again under the same instrumental conditions. Results showed very good contrast and best phase discrimination with the use of metallic filter, iodine as dopant and the highest spatial resolution obtained for smallest sample used.