The knowledge of size, density and both orientation and vertical distribution of fractures as well as their opening and filling material or overburden thickness is a valuable contribution to estimating hydraulic conductivity and to evaluating the vulnerability and protection strategy of karst aquifers. To obtain some of these parameters and to as certain high-permeability zones, the Very Low Frequency-Electromagnetic Gradient (VLF-EM GRAD) method was applied, together with Radio Frequency-Electromagnetics (RF-EM), Radiomagnetotellurics (RMT), Geoelectrical Tomography and refraction seismics, over a karstic terrain in the Swiss Jura Mountains. In this area, karst springs infiltrate a porous aquifer. This survey investigated the highly permeable karst structures, which provide fast water-infiltration pathways into the karstic flow network. Adye tracer test validated the geophysical results. The results show the efficiency and reliability, particularly of the VLF-EMGRAD method, for high-resolution investigation at shallow depths and for its potential for fast data acquisition over large surfaces at catchment area scale without ground contact.