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 ascertain 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. A dye tracer test validated the geophysical results. The results show the efficiency and reliability, particularly of the VLF‐EM GRAD 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.