Three different-scale electromagnetic (EM) measurements have been performed in the Kujukuri coastal plain, southeast Japan, to investigate the distribution of saline groundwater. The three techniques were audio-frequency magnetotelluric (AMT), transient electromagnetic (TEM), and small loop-loop EM measurements. The resistivity sections estimated from these data sets reveal three independent resistivity distributions extending to different depths. The AMT method reveals a regional-scale resistivity distribution across the plain to a maximum depth of approximately 500 in and the existence of deep conductive zones, which are inferred to be associated with fossil seawater trapped in a Pleistocene formation. The TEM results show a medium-scale resistivity distribution to depths of approximately 100 m, in which two shallow conductive zones are recognized. It is concluded that these features are caused by present seawater intrusion and high-salinity salt-marsh deposits formed during sporadic marine regressions. The small loop-loop EM method provided a shallow resistivity profile that highlights the conductive salt-marsh deposits and resistive sandy ridges. Although these resistivity sections correspond to different depth ranges, the overlapping portions of the sections are very consistent with one another. These EM methods are useful in detecting and interpreting important resistivity features. Taking the geologic evolution of the coastal plains into consideration is crucial when interpreting resistivity profiles such as these, and our results suggest that the presence of fossil seawater is an important factor controlling resistivity at a variety of depths.