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In large mountainous catchments, shallow unconfined alluvial aquifers play an important role in conveying subsurface runoff to the foreland. Their relatively small extent poses a serious problem for ground water flow models on the river basin scale. River basin scale models describing the entire water cycle are necessary in integrated water resources management and to study the impact of global climate change on ground water resources. Integrated regional-scale models must use a coarse, fixed discretization to keep computational demands low and to facilitate model coupling. This can lead to discrepancies between model discretization and the geometrical properties of natural systems. Here, an approach to overcome this discrepancy is discussed using the example of the German-Austrian Upper Danube catchment, where a coarse ground water flow model was developed using MODFLOW. The method developed uses a modified concept from a hydrological catchment drainage analysis in order to adapt the aquifer geometry such that it respects the numerical requirements of the chosen discretization, that is, the width and the thickness of cells as well as gradients and connectivity of the catchment. In order to show the efficiency of the developed method, it was tested and compared to a finely discretized ground water model of the Ammer subcatchment. The results of the analysis prove the applicability of the new approach and contribute to the idea of using physically based ground water models in large catchments.