We test the integration of ground-penetrating radar (GPR) borehole investigation and electromagnetic flowmeter surveys to characterize fissured or complex aquifers. Borehole GPR investigation allows assessment of the lateral continuity of the porous and permeable zones between closely spaced boreholes, whereas flowmeter tests are adopted to identify the inflow–outflow zones in the boreholes. We apply the coupled approach in a portion (between 10 and 20 m below ground surface) of a complex aquifer hosted in a calcareous–gypsiferous formation. The hydro-geophysical characterization was aimed to detect the most conductive levels and to estimate the hydrodynamic properties of the aquifer. The integration of single-hole flowmeters and GPR measurements accurately distinguished different productive levels of high porosity and permeability in the aquifer. Two aquifer systems characterized by a complex geometry of fissures and permeable layers have been recognized, establishing the role of the drilled boreholes in the short-circuiting of the two systems. Interpretation of the GPR survey in cross-hole configuration gave values of total porosity of the order of 0.35 and 0.5 in the two more productive levels, which were detected by the flowmeter investigation.