Water deficit and salt accumulation in soil presents serious problems to crop production in semi-arid regions. These problems depend on the active transpiration stream and the selective absorption of ions by crop roots. In this study, a large sized soil column system was used to examine the dynamics of water and ion transport and salt accumulation in soil layers. Special reference was placed on the effects of the active and selective absorption by roots of different crops (i.e., corn plants, sunflower plants and no plants). The column system was equipped with on-line systems for the control of groundwater level. Soil water content sensors enabled time-course evaluations of the volumetric water content and hence upward flux of the groundwater in the soils at different depths. Furthermore, the distribution and accumulation of ions in soil layers, plant organs and xylem sap were analyzed using ion chromatography. In this column experiment, diurnal and longer term changes in water movement and ion accumulation in soil, affected by root absorption characteristics of plants, were evaluated quantitatively. The results demonstrated that the column system was applicable for the quantitative analysis of the effects of root absorption by different crops on water deficit and salinization in soils.