Soil salinity and sodicity are escalating problems worldwide, especially in arid and semi-arid regions. A laboratory experiment was conducted in soil columns to investigate redistribution of soluble cations through soil profile after reclaiming process of a calcareous saline sodic soil (CaCO3 = 20.7%, EC = 19.8 dS m−1, SAR = 32.2 (meq L−1)0.5). Two series of reclamation experiments, consisting of soil and water treatments were applied. The soil amendments were comprised of control, cattle manure (50 g kg−1), pistachio residue (50 g kg−1), gypsum (5.2 g kg−1; equivalent of gypsum requirement), manure + gypsum and pistachio residue + gypsum. After one month incubation, two types of water quality, including untreated and treated with sulfuric acid, were applied with irrigation for four months. The results showed that the concentration of all monovalent and bivalent cations as well as EC and SAR differed significantly (α = 0.01) among soil amendments. In contrast, the effect of applied sulfuric acid in the irrigation water was negligible on the final soil EC, but it was significant on soil SAR. Soluble Na+ and K+ showed a higher mobility than Ca2+ and Mg2+ within the soil. At the end of experiments, soil EC and SAR decreased significantly even for the unamended soil. This can be caused by solute leaching. In absence of sulfuric acid, pistachio residue was the best amendment in reducing soil EC and SAR. This study brings up some synergistic or antagonistic behaviors between gypsum and organic amendments in particular for the monovalent cations.