A three-dimensional (3D) groundwater flow model of the deep multi-aquifer Quaternary deposits of the Po plain sedimentary basin, within a 3,300-km(2) area (Veneto, Italy), is developed, tested and applied to aid sustainable large-scale water-resources management. Integrated mathematical modelling proves significantly successful, owing to an unusual wealth of available geological, geophysical, and hydrologic data and to state-of-the-art numerical tools. Of particular interest is the evaluation of the influence of alternative conceptual models; that is, of reconstructed representations of the 3D geological model of the structure of the aquifers. The reference conceptual model is set up by means of extended geological sections and stratigraphic records, and is used to create a large, unstructured 3D finite element grid. By analyzing the effects on piezometric surfaces and on the overall water budget of geometrical perturbations from the reference structure, alternative geo-structural models, obtained by systematically shifting the pinch-out of the aquitards, are compared. Interestingly, the impacts of aquitard pinch-out prove far from negligible. The results suggest the critical importance of reliable geological models even for large, complex 3D models. The good practice of iteratively testing numerically the impact of surprises on the conceptual model, as more field information is collected, is thus supported.