Increasing pressure on water resources, associated with climatic changes, is a significant challenge for the agricultural activities in the studied region. Hence, in order to preserve fresh water, local farmers are in obligation to use marginal water qualities for supporting agricultural production. In the study area, since four years, local farmers have been using treated wastewater and saline groundwater for irrigation. The objective of the study is to evaluate the changes in soil properties and geochemical behavior of chemical elements according to the irrigation water qualities by using enrichment factors and isovolumetric mass balance as survey tools. In three selected plots, a vertical soil sampling is made as a pedological profile in the irrigated soils and the non irrigated one. The total bulk contents of chemical elements in soils as well as some physicochemical properties were characterised. Then, the contents of major and metal elements are used to calculate the enrichment factors (EF) and isovolumetric mass balance as qualitative and quantitative tools respectively. These two parameters are used to evaluate the vertical distribution and mobility of chemical elements in soils with regard of physicochemical properties. According to the findings, irrigation with treated wastewater improved soil properties and increased the bulk contents of chemical elements. Moreover, the major and metallic elements are leached down into particular and exchangeable forms, and then accumulated in the depth as a new soil layer. This trend is confirmed by the increase in the isovolumetric stocks of all these elements in the soil profile. Moreover, using treated wastewater at a high irrigation rate enhances the pedogenesis process and results in increased soil chemical element stocks, improved soil fertility, and aggregates stability. By contrast, the irrigation with groundwater caused a decrease in soil pH and an acceleration of the decarbonation process. As a result, soil aggregates are dispersed, chemical elements are dissolved and transported out of pedon. This is confirmed by the negative isovolumetric stocks calculated for this site. Besides, the irrigation with saline groundwater causes the loss of all chemical elements of the soil due to degradation and dissolution of soil aggregates which could lead to a short-term decrease in soil fertility and stability. The findings are a valuable tool for determining soil contamination or degradation, and can be used in future monitoring programs to ensure soil quality.