The use of geophysical characterization of karst systems can provide an economical and non-invasive alternative for extracting information about cavities, sinkholes, pathways for water infiltration as well as the degree of karstification of underlying carbonate rocks. In the present study, three geophysical techniques, namely, Ground Penetrating Radar (GPR), Electrical Resistivity Tomography (ERT) and Very Low Frequency Electromagnetic (VLFEM) were applied at three different and appropriate locations in fluvial karst of a listed environmentally sensitive area of the Rio Vermelho, Mambaí, Goiás, Brazil. In the data acquisition phase, the GPR, direct-current (DC) resistivity and VLFEM profiles were obtained at three different locations in the area. Data were analyzed using commonly adopted processing workflows. Different radar typologies have been assigned to soil and rock typse. The GPR results showed a well-defined lithology of the site based on the amplitude of the signal. On the other hand, the inverted resistivity cross-sections showed a three-layered stratigraphy, pathways of water infiltration and the weathered structures in carbonate (Bambui group). The interpretation of VLFEM as contours of current density resulted from Fraser and Karous-Hjelt filters, indicate the presence of conductive structures (high apparent current density) that may be linked with the weathered carbonate and other conductive and resistive anomalies may be associated with the water-filled and dry cavities (cave). The results encourage the integrated application of geophysical techniques as the reconnaissance for further detailed characterization of the karst areas.