The article presents non-destructive testing based on electrical impedance tomography (EIT) for spatial (3D) monitoring of flood embankments. Therefore, to solve the inverse problem of the EIT, an effective algorithm based on multiple elastic nets has been developed. The originality of the solution is based on the application of many elastic net algorithms as functions, each of which, based on the vector of all measurements, generates the value of a single pixel for the reconstructed image. In this way, the set of elastic nets is equal to the resolution of the image output. Such an approach, although requiring more computing power, yields high resolution images. In addition, the presented algorithms are characterized by high noise immunity and distortion of measurement data. Five different electrode systems were tested in the samples and compared with each other in two measurement variants (stimulations). A reconstruction made on the basis of actual measurements obtained from the physical model was also presented. The presented solution provides a visual analysis of seepages and leaks, which allows for quick and effective intervention and possible prevention of dangers. The research proved that the use of tomographic measurement techniques in combination with the image reconstruction algorithm based on elastic net allows for non-invasive and very accurate spatial assessment of leaks and damages of flood embankments. The received results confirm the effectiveness of the presented research.