The coupling of soil and root water fluxes at the plant scale is a particularly challenging task. Numerical three-dimensional plant-scale models exist that consider these soil–root interactions. The influence of the hydraulic conductivity drop at the microscopic scale and especially the effect on root water uptake is not yet assessed in such models. In this study, an analytical approach describing the hydraulic conductivity drop from the bulk soil to the soil–root interface for a three-dimensional plant-scale model was derived and validated by numerical means. With these tools, quantification of the local hydraulic conductivity drop with time was possible. Furthermore, the effect of the hydraulic conductivity drop on the time occurrence of plant stress was evaluated. Root water uptake was assessed, with and without considering the hydraulic conductivity drop around single roots in a three-dimensional plant-scale model in terms of total water uptake at the root collar under different soil and root properties. It was shown that the total root water uptake was strongly affected, especially under conditions where the radial root hydraulic conductivity, which regulates root water uptake, was larger than the soil hydraulic conductivity, which regulates water flow in the soil. These findings were backed up by numerical validation of the model using mesh refinement. Incorporation of the hydraulic conductivity drop around individual roots in a three-dimensional plant-scale model can solve problems with greater accuracy for larger grid resolutions, and with smaller computational times, than not considering the hydraulic conductivity drop.