Crystalline rocks are generally characterized by negligible porosity and permeability in terms of groundwater exploitability. However, alteration processes can greatly increase their fracture permeability and induce formation of modest, but locally important aquifers. Therefore, subsurface characteristics of alteration zones are of major importance for hydrogeological evaluation of crystalline terrains. Alteration processes greatly affect rock total porosity and water content, causing contrasting electrical resistivity of rocks affected by varying degrees of weathering. This makes electrical resistivity tomography (ERT) a preferable geophysical method for the exploration of alteration zones in crystalline rocks. In our research, we used an integrated approach, combining the ERT method with monitoring of spring discharge and hydrochemistry to characterize metamorphic aquifers on slopes of the Medvednica Mountain (Croatia). Significant fracture flow aquifers are found to be formed in intensely fractured but not highly weathered rock masses (medium to high resistivity values), while highly weathered masses (low resistivity values) form local barriers for fracture flows. Subsurface structure of the alteration zone proved to be highly irregular, with sharp contacts between more and less weathered rocks. Decrease of permeability below the alteration zone keeps the water level near the surface and enables spring occurrence on the mountain slopes. Studied aquifers have relatively limited extent, resulting in typical capacity of major springs of a few l/s. More frequent but less productive springs are attributed to the draining of the shallow part of the alteration zone (mostly saprolite). Combination of the ERT method with spring monitoring proved to be very effective as a first and relatively inexpensive methodology for hydrogeological characterization of crystalline terrains, both in local and catchment scales.