A 2D physically based framework is proposed to analyze the effect of a non-uniform water supply at the soil surface generated by rainfall interception and stemflow on soil-root water transport in the case of heterogeneous distribution of the roots in the soil profile. To model soil-root water transport, the root water potential of two plants placed in two adjacent rows was simulated so as to minimize the difference between the evaporative demand and the amount of water taken up by each plant. A characterization of the throughfall to incident rainfall, soil hydrodynamic properties, soil-root contacts, and maize evapotranspiration, was carried out during a 10-day experiment with a leaf area index of about 4 to 5 m2 m−2. Mean rainfall interception percentages were in the [47.4%–52.6%] range at half the distance between two adjacent rows, whereas an interception percentage higher than 80% was found near the stems along the rows. As a result, the mean estimated stemflow was 1 L per plant per 16.4 mm water supply above the canopy. Good agreement was found between the measured and predicted transpiration values. As the soil started to moisten, the predicted root water potential rapidly increased, in line with the predicted number of active roots that rapidly decreased. Effects due to stemflow during infiltration disappeared progressively when drying was in progress. The proposed approach could be useful for analyzing soil-root water transport and possible pollution when solutes move with water under various realistic conditions where non-uniform water supply is involved.