After the 2011 Tohoku earthquake, thirteen thousand hectares of farmlands were damaged by massive Tsunami near coastal sites in Miyagi, Japan. Some eighty percent of the damaged farmlands have been recovered in 2014, but subsidence and high salinity groundwater make it difficult to completely remove salinity from the soil. To solve the problem, management of saltwater intrusion plays an important role in rootzone salinity control with the Field Monitoring System (FMS), which is remote sensing technology of wireless real-time soil data through the internet data sever to investigate high soil moisture and high salinity in tsunami affected fields. Using the FMS with the time domain transmission system, we monitored soil moisture, electrical conductivity (EC), groundwater level, and EC of groundwater at tsunami damaged paddy fields. The field measurements of the FMS were conducted at two sites of tsunami damaged farmlands in Iwanuma and Higashimatsushima of Miyagi prefecture, Japan. After the Tohoku disaster, co-seismic subsidence of 17–21 cm and 50–60 cm of the land was reported at the sites, respectively. Our findings were high EC of groundwater (> 35 dS m<sup>−1</sup>) due to intrusion of sea water into groundwater in 2013. Although the shallow groundwater provided salinity to the soil surface in 2014, the FEM allowed us to monitor high EC (< 6 dS m<sup>−1</sup>) even in saturated soil condition. Rainfall facilitated desalination process, but the saline groundwater level reached the soil surface after heavy rainfall, suggesting that coastal zone aquifer management is essential to prevent saltwater intrusion into groundwater.