Geophysical methods are non-invasive and allow an effective way of understanding subsurface structures and their physical properties. One of the main challenges in this is the non-uniqueness of the geophysical models and that several different models can explain a dataset to an agreeable fit. Moreover, noise and limitations in resolution, which are inherent to field data, are additional obstacles for obtaining a true physical model of the subsurface. Facing all these challenges, radio-magnetotelluric (RMT), boat-towed RMT, boat-towed controlled source MT (CSMT), electrical resistivity tomography (ERT) are jointly used for fracture zone delineation under shallow water-bodies. The joint approach, as compared with any individual method, shows a better ability to both resolve the geological targets and to assist in understanding the subsurface geology that hosts these targets. For examples: by performing the joint inversion of lake-floor ERT and boat-towed RMT data, a fracture zone is better delineated with greater details compared with single inversions; by employing boat-towed CSMT measurements and jointly inverting with boat-towed RMT data, the subsurface structures are better resolved than by inverting each dataset alone. The studies are useful for near-surface applications including, for examples, engineering purposes such as planning of underground infrastructures, site characterization in connection with energy or waste storage, and geohazard investigations.