A multidisciplinary method for characterizing fractured aquifers is conducted on the base of two different aquifers: Plancoët in crystalline context and Quézac in carbonate context. It consists first to analyse the geological context and construct a geometrical model of the aquifer at various scales, on the base of image analysis, field observations and geophysical prospecting. Geometrical models that are realised take into account the specific particularities of both sites. Then an analysis of hydrologic, hydrogeologic and geochemical characteristics is realised for Plancoët, which leads to settle a hydrogeological model that confirms the geological structure and helps to locate a new pumping well. The pluridisciplinarity of the methods in this work helps to well understand the studied aquifers.