The problem of salt-ravaged lands is reported in many parts of the world and could be exacerbated by the presence of an endorheic pond normally associated with a saline low-lying area. An endorheic or playa pond accumulates dissolved salts which can be carried primarily by groundwater before discharging into the pond; then, intense evaporation produces salt residues which can wreak havoc on the adjacent areas. The objective of this study is to investigate the subsurface conditions and groundwater interactions beneath two endorheic saline ponds of Thailand’s Great Mekong Basin to have a better understanding and thereby efficiently manage the resources. A comprehensive analysis of the physical and geochemical properties (limited to pH, specific conductance and salinity) of the subsurface system was performed to determine the processes that regulated the migration of dissolved salt. The data collected from the deep and shallow groundwater of the basin were analyzed to determine their physical and chemical properties. Soil samples of various depths were examined to determine their respective geologic, chemical and unsaturated properties. The groundwater near the salt ponds was different from that of other areas in that its groundwater table was closer to the surface soil and its deep groundwater, which is of high pressure, was more saline than its shallow groundwater. As the capillary rise influences the topsoil, particularly in the saline pond areas, the vertical upward flow and the capillary force are thus the additional mechanisms of salt transportation to the endorheic ponds. Since these surface water bodies are the discharge sites for saline groundwater and are not perennial, a practical solution is to localize the saline groundwater.