To estimate a layer thickness of freshwater and displacement of saltwater in a sandy coastal aquifer, a technique using time domain reflectometry (TDR) was developed for measuring groundwater level and freshwater/saltwater interface level. TDR probe was of coaxial type having 67.5 cm in length and 3 cm in diameter. The tip of the probe was designed to be a cone form for insertion into deep sandy layer. Laboratory column tests were carried out to examine the technique. Dune sand obtained in Tottori, Japan, was packed in the column and the probe was vertically set under ground. To reproduce the actual aquifer situation, the groundwater level or the interface level were fluctuated by controlling the supplies and extractions of freshwater or saltwater at the bottom of the column. During the level fluctuations, to measure TDR waveforms, microwave step-pulses were applied to the probe from the TDR cable tester. From the waveforms, we sampled the pulse travel time between root and tip of the probe and the travel time through fresh water, from which we can estimate the groundwater and interface levels, respectively. The experimental results showed that the new technique presented good estimations of groundwater and interface levels. In conclusion, the technique may be useful for monitoring the layer thickness of freshwater and the interface level fluctuation affected by seawater intrusion in a sandy coast.