We present an innovative hydrogeophysical approach for non-invasive quantification of the unsaturated water flow. For the water content measurements, we apply the Magnetic Resonance Sounding (MRS) method in the time-lapse mode. For inversion of MRS measurements, we approximate the subsurface by a horizontally stratified media. Laterally, the MRS estimated water content is averaged over the area below the measuring setup. During this study, we used a square loop of 75 m side-length. The time-lapse inversion allows visualizing variations in the water content in the vadose zone down to twenty meters. We tested our approach at the Villamblain test site (France). For that, we carried out the MRS monitoring in 1999–2000 and 2020–2021. During these two observation windows, MRS shows seasonal variations of the water content but also a strong dependence of the water content on the rainfall that was different between two data sets. Comparison of MRS results with the rainfall records shows a good correspondence in-between. For measuring and processing MRS data, we used commercially available MRS instrument and interpretation software.