Abstract The selection of the best possible method to interpolate a continuous groundwater surface from point data of groundwater levels is a controversial issue. In the present study four deterministic and five geostatistical interpolation methods (global polynomial interpolation, local polynomial interpolation, inverse distance weighting, radial basis function, simple-, ordinary-, universal-, empirical Bayesian and co-Kriging) and six error statistics (ME, MAE, MAPE, RMSE, RMSSE, Pearson R) were examined for a Jurassic karst aquifer and a Quaternary alluvial aquifer. We investigated the possible propagation of uncertainty of the chosen interpolation method on the calculation of the estimated vertical groundwater exchange between the aquifers. Furthermore, we validated the results with eco-hydrogeological data including the comparison between calculated groundwater depths and geographic locations of karst springs, wetlands and surface waters. These results show, that calculated inter-aquifer exchange rates based on different interpolations of groundwater potentials may vary greatly depending on the chosen interpolation method (by factor >10). Therefore, the choice of an interpolation method should be made with care, taking different error measures as well as additional data for plausibility control into account. The most accurate results have been obtained with co-Kriging incorporating secondary data (e.g. topography, river levels).