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Characterizing the hydrogeological functioning of complex crystalline aquifers requires a precise assessment of their structural and hydrodynamic heterogeneities. This study shows how the joint use of TDEM, ERT and MRS enables to characterize both alterites and weathered-fissured zones. Moreover, with complementary data such as water table measurements and hydraulic tests, the characterization of the fractured zone is also possible. A conceptual hydrogeological model is then proposed from a case study in India, thanks to this joint use of geophysical and hydrological data.