The spatial distribution of confining layers within a system of two aquifers strongly affects the hydraulics and sensitivity to pollution. The test site is located close to a well field. Wells are switched with short intervals and hydraulic heads are recorded in several observation wells. Because the absolute levels of simulated hydraulic heads do not always coincide with the measurements, the model is calibrated with short term head variations. The characteristic shape of the hydraulic heads at each observation wells contains sensitive information about the structure of the aquifer. A numerical technique is developed which enables to simulate the spatial distribution of the confining layer. The method comprises the use of pilot points and regularisation technique. Cross validation is carried out in order to show the results are physically based. The method is shown to provide significant results even under non optimal conditions.