In Koh Thom district, people mostly rely on agriculture for their incomes. The irrigation systems are based on prek namely small channels diverting the water of the Bassac River in the floodplain. This system potentially contributes to changing the flood dynamics in the area by reducing the period of submersion and its amplitude. This may change the relationships between surface and groundwater flow, with potential pollutant accumulation in aquifers, but this has never been studied in detail. Very few hydrological observations are available in the area, but ground electrical conductivity (EC) measurements can provide some answers about infiltration processes or water transfers because it depends on the water content, mineralization and matrix type. For a given lithology, any change in ground EC can be interpreted as changes in terms of water movement or mixing. A detailed geophysical survey using frequency electromagnetic method (FEM) was conducted to measure the apparent ground EC from the surface. The soundings were conducted between two preks, one rehabilitated (deepened and equipped with a gate), prek Chann, and one traditional, prek Touch. The geophysical equipment (CMD-explorer) provides simultaneous soundings at 3 depths but is limited to 6 m deep. Apparent ground EC sounding were carried out, the 2D maps were calculated, and ground EC vertical panels were simulated using IX1D inversion of the soundings. The apparent ground EC ranged from 0 to 210mS/m, clearly increasing with depth and towards the low-lying areas. Inversion modeling produced cross-section panels suggesting the presence of a conductive layer at 4m below the ground surface overlain by a resistive layer with lateral variation of the conductivity, namely more resistive in the low- lying areas. This layer could be interpreted as vadose zone leaching from percolated water since it corresponds to areas where water from excess irrigation return flow accumulates on the surface. This mechanism contributes to the connection between surface water and groundwater in the area in the dry season and may imply pollutant dissemination and transfer from the surface to groundwater. Since groundwater is largely used for domestic purposes, more investigations should be conducted to evaluate the potential health risks.