The Volvic natural mineral water is catched in a complex volcanic aquifer located in the northern part of the “Chaîne des Puys” volcanic system (Auvergne, France). In the watershed, water transits through scoria cones and basaltic to trachybasaltic lava flows. These aa lava flows, emitted by strombolian cones between 75,000 and 10,000 years ago, are emplaced in deep paleovalleys incised within the variscan crystalline bedrock. The volcanic infill is highly heterogeneous. In order to build a hydrogeological model of the watershed, a simple but robust methodology was developed to reconstruct the bedrock morphology and the volcanic infill in this paleovalley context. This methodology, based on the combination of genetic and geometric approaches, appears to be rather efficient to define both the substratum and the lava flows geometry. A 3D geological model is then proposed. It synthesizes the data from 99 boreholes logs, 2D geoelectric profiles, morphologic clues, datings and petrographic data. A genetic approach, integrating aa lava flow morphology and emplacement behaviour, was used to reconstruct the chronology of the volcanic events and lava flow emplacement from the upper part of the Dômes plateau to the Limagne plain. The precision of the volcanic reconstruction is discussed: the main limitation of the methodology are related to the homogeneity of the petrographic and geochemical composition of the lava flows succession (except for the trachyandesitic Nugere lava), the spatially variable borehole density, the lack of a real petrographical and geological description on most of the available geological logs. Nevertheless, the developed methodology combining spatial and genetic approaches appears to be well adapted to constrain complex lava flow infill geometries in paleovalley context.