Since the 2011 Tohoku earthquake in Japan, natural rainfall has helped to reduce the salinity levels in the root zone of agricultural fields. However, leaching resulting from natural rainfall alone was insufficient for crop management in tsunami-affected regions, where severe subsidence had occurred. In order to understand the desalinization process, a Field Monitoring System was installed with time domain transmission, a sensor network technology used to investigate high soil moisture and high salinity levels in a tsunami-affected field in Miyagi. Using the Field Monitoring System with time domain transmission, volumetric soil water content and bulk soil electrical conductivity was monitored in tsunami-damaged farmland before-and-after the application of two weeks of the flooded leaching method with the addition of a topsoil layer. Pore water electrical conductivity may be estimated based on volumetric soil water content and bulk soil electrical conductivity using the Rhoades model. During the flooded leaching period, in situ bulk soil electrical conductivity dropped above the deeper groundwater but did not decrease near the boundary between the added topsoil and the salt affected cracking subsoil. This indicates that preferential flow may have occurred, and flooded leaching was not enough to reduce the salinity level near the boundary. Pore water electrical conductivity was an excellent indicator of whether the field's salinity level was low enough to maintain moderately salinity sensitive crops such as rice and soybean through Field Monitoring System real time monitoring.