To understand how water uptake locally affects and is affected by the soil water distribution, three-dimensional soil–root models need to be developed. Nowadays, fully coupled three-dimensional soil–root flow models at the plant scale are available that simulate water flow along water potential gradients in the soil–root continuum, but the problems that arise by the coupling of soil and root have not been investigated thoroughly. In a previous work, we introduced and numerically validated a microscopic model to be used on a coarse numerical soil grid, describing the hydraulic conductivity drop between the bulk soil and the soil–root interface within a voxel of a three-dimensional soil–root model. In this study, the impact of the local hydraulic conductivity drop on denser root architectures and in drier soil regions was assessed. When a coarse discretization of the soil grid is used, the local hydraulic conductivity drop has a significant effect on the water potential distribution at the soil–root interface and in the xylem, especially under conditions near plant stress where the local soil conductivity is lower than the radial root conductivity regulating root water uptake. As a consequence, plant stress conditions will be reached earlier than if the local conductivity drop within a soil voxel is neglected. In comparison with a fine soil discretization, the soil water potential gradient calculated by including the local conductivity drop at a coarser discretization does not fit the soil water potential gradient resulting from the fine soil discretization. Estimation of accurate water potential gradients throughout the soil requires a fine soil discretization.