The development of the wet bulb under drip irrigation in sand-covered soils presents a different behavior compared to the one observed in homogeneous soils. Moreover, the presence of a very active crop imposes a series of variations that have not been fully characterized. The aim of this work is to present the data acquisition methodology to calibrate and validate the Hydrus-3D model in order to safely define the evolution of moisture in wet bulbs generated in stratified “sanded” soils characteristic of greenhouses with intensive pepper crop under drip irrigation. The procedure for collecting and processing moisture data in stratified soils has been defined. Soil permeability; retention curve, texture, and bulk density have been measured experimentally for each material. It has been found that the inclusion of a previous day in the simulation improves model predictions of soil moisture distribution. In soils with less gravel, a lower average stress and a more homogeneous moisture distribution were observed. It has been proved that the Hydrus-3D model can reproduce the behavior of sand covered soils under intensive greenhouse growing conditions, and it has been possible to verify that the predictions are adequate to what has been observed in the field. In view of the results, the Hydrus-3D model could be used to establish future irrigation strategies or to locate the optimal placement point of tensiometers that control irrigation in sandy soils for intensive agriculture.