Subsurface temperature is a key parameter for geothermal energy prospection in sedimentary basins. Here, we present the results of a 3D temperature modelling using a thermal-tectonic forward modelling method, calibrated with subsurface temperature measurements in the Netherlands. The first step involves the generation of a coherent dataset of temperature values for the calibration of the model. In the Netherlands, most of the available measurements (98.8%) are BHT measurements and therefore need to be corrected from the thermal perturbation created during drilling. The remaining 1.2% is composed of DST measurements, which closely resemble the formation temperature (i.e., ±5 °C). The resulting dataset, after correction, gives a total number of 1293 values in 454 wells. Included in this dataset are 412 highly reliable values corrected with the Instantaneous Cylinder Source (ICS) method and 829 values of a lower reliability corrected with the AAPG method. In addition to the corrected values, 52 DST values in 26 wells are available from the Dutch subsurface. The average thermal gradient of this whole dataset is 31.3 °C/km with a surface temperature of 10.1 °C. The second step in the modelling process was the generation of a 3D forward model that focuses on calculating the temperature distribution of the sedimentary basin fill, taking into account the basin evolution of the past 20 Myrs and thermal properties and processes of the whole lithosphere. From the 3D thermal model, we extracted 2D cross sections across well locations to compare model temperatures with calibration data. Furthermore, we present vertical profiles, isodepth maps and temperature projection on geological layers, to discuss the relationship between temperature and geology. Anomalies in this relationship can have several causes and include: 1) the extreme thermal conductivity and complex geometry of the Zechstein salt; 2) enhanced radiogenic heat production of the upper crust due to magmatic intrusions. In addition, our model supports earlier findings that shallow hydrothermal convection in highly permeable sediments can effectively lower thermal conductivity and temperatures in shallow sediments.