Geological deformations like anticlines have a prominent role in aquifer system functioning. Structural deformations control erosion patterns, areas of nondeposition, lateral facies variations and thickness variations. The nature and geometry of geological bodies have a major impact on the aquifers and interconnections between them. To characterize these features and to quantify their influence on overall hydrogeological functioning, a multidisciplinary approach is proposed at a local scale. In southwestern France, the Aquitaine Basin contains a regional multilayered aquifer system affected by numerous anticlines. The Villagrains-Landiras anticline is a major anticline of the Aquitaine Basin, and near its axis is the subcropping Cenomanian aquifer; thus, the Cenomanian aquifer has potential for drinking water supply. An extensive research program was developed, including reconnaissance drilling, water level measurements, geochemical analyses, and petrophysical tests, and the results were combined with existing data. This integrated work precisely defined the complex architecture of the aquifer and confining units linked with the uplift and the polyphase erosion of the anticline. It resulted in the characterisation of the deposits’ geometries, lithology, and aquifer properties. The areas of aquifer interconnection have been defined and recharge flows have been estimated. A new groundwater circulation pattern constrained by isotopic water residence times was developed. A new geological model was built, which enables a rethink of the local functioning of the aquifer targeted for drinkable-water supply, but also it allows an understanding of the importance of anticline structure on the recharge conditions of the aquifers of this regional multilayered aquifer system.