This paper discusses characterizing and validating potential sites for high level radioactive waste disposal along the coastal areas using newly developed geophysical prospecting tools. The specific objective of this paper is to develop an electromagnetic (EM) technology for investigating the subsurface to the depths of 1, 000 m below the seafloor in the near-shore environment. The depth to the sea floor is up to 200 m. Characterization and validation of a site for high level radioactive waste disposal require a detailed knowledge of both the geological structures and the groundwater characteristics. The commercial as well as research-based marine controlled-source and natural-source EM technologies are available, however, there has been little work done in shallow water depths environment using such technologies. Here, we report the state-of-the-art EM method with applications to coastal areas with shallow water depths environment. Marine EM instrument developed is appropriate for investigating shallow water environment near coastal area. The interpretational technology for EM data is focused on 3-D magnetotelluric (MT) and 2.5-D controlled-source electromagnetics (CSEM). This paper demonstrates the performance of the new type of instrument and software, and the field experiment that was carried out in the Monterey Bay of California, USA, in 2003 and 2004. Additionally, we demonstrate interpretation techniques applied to characterizing groundwater using MT3-D result of Horonobe, Hokkaido.