In agricultural lands has the soil moisture uptake from the root system a significant effect on the water regime of the soil profile. In texturally heavy soils, where preferential pathways are present, infiltrated precipitation and irrigation water with diluted fertilizers quickly penetrate to a significant depth and often reach an under-root zone or even the ground-water level. Such a scenario is likely to happen during long summer periods without rain followed by heavy precipitation events, when a part of the water may flow through desiccated cracks.Since 2001 the effects of drip irrigation and nitrogen fertilization of potatoes (Solanum tuberosum L., cultivar Agria) have been monitored within the frame of a research project at the experimental site Valecov (Czech Republic). Based upon the measured data an attempt has been made to simulate the water regime of the soil profile at a selected experimental plot, considering the impact of preferential flow and root water uptake. The dual-permeability simulation model S_1D_Dual (VOGEL et al., 2000) was used for the simulation. The soil hydraulic parameters were inversely determined using Levenberg-Marquardt method. Measured and simulated pressure heads were utilized in the optimization criterion. The scaling approach was applied to simplify the description of the spatial variability of the soil profile.The results of simulations demonstrate that during particular rainfall events the water reaches significant depths of the soil profile via preferential pathways. The effect of the root zone is dominant during dry periods, when capillary water uptake from the layers below roots becomes important. This should be taken in account into the optimization of the drip irrigation and nitrogen fertilization schedule.