Use of parameter estimation techniques is nowadays commonplace in groundwater model calibration. However, many difficulties are encountered when it comes to characterize the distribution of hydraulic conductivity. The purpose of this work is to demonstrate a practical methodology of pilot points for characterizing hydraulic conductivity variability in the heterogeneous aquifer at Lauswiesen test site, which is located close to the city of Tübingen, Germany. Pilot points allow a great deal of flexibility in the disposition of areas of high and low hydraulic conductivity value to be identified through the calibration process, in which there is no more need for the modeler to guess the geometry of hydraulic conductivity distribution prior to model calibration. The results indicate that the structure of the aquifer estimated using pilot points has a very similar trend to the previously performed field experiments at the site. It was also verified that pilot points are very powerful to capture high heterogeneous geological formations, whereas analytical solutions were only able to conclude almost homogenous case.