The flood levees in the vicinity of Krakow city (Poland) are, in some places, over 100 years old. Thereupon, in the flood dike, and its subsoil, can appear unconsolidated zones, which, during the flood stage, can be a simple way of water flow and/or even can be the place where the levee body will be destroyed. This phenomenon took place in Wawrzeńczyce village, near Krakow city, during the flood in 2010. The geophysical research was carried out, in order to develop a methodology of recognition of potential areas where the levee body can be damaged. The geophysical surveys were conducted with the use of electrical and electromagnetic methods, as well as utilizing the seismic method. The general identification of examined media was realized by the electrical resistivity tomography (ERT) method. The ERT surveys were supplemented by capacitively-coupled resistivity (CCR) measurements, in order to analyze the usefulness of the CCR method for the examination of river dikes and reduction of interpretation ambiguity. The ground penetrating radar (GPR) method detected small anomalies in the body dike, due to the very high resolution of this method, which were not detected by the ERT and CCR techniques. During GPR surveys, non-standard measurement techniques were applied. Finally, the high-resolution seismic reflection (HRSR) method provided a clear and high-resolution image of the dike structure up to the water table and assisted with the identification of the hazard non-consolidated zones.