The role of calcium (Ca)-containing amendments in ameliorating the deleterious effects of sodium (Na) on soil hydraulic conductivity and infiltration rates has been extensively studied. Nevertheless, the effect of indigenous calcite itself on Na-saturated soil (clay) systems has not been clearly documented yet. The effect of calcite dissolution from different calcite (Ward's standard 46-W-1435-PAC) containing columns and the ameliorative effects on Na-saturated clayey (SWy-1 montmorillonite) systems was examined from two different perspectives: i) leaching the columns with Na/Ca solutions of SAR 10 (sodium adsorption ratio), and ii) leaching the same columns again using deionized water (simulating the process in which rainfall percolates through Na-affected calcareous and noncalcareous soils). As the columns were leached with SAR 10 water, the SAR of the leachates decreased, and the pH increased considerably with the calcite dissolution. A higher level of carbon dioxide in the SAR 10 water drastically increased the effect of calcite in reducing exchangeable sodium percentage. When deionized water was applied to the columns, the pH values were about 10, and calcite dissolution was enhanced. With the calcite-containing columns, a linear relationship between electrical conductivity and hydraulic conductivity was found during the leaching with deionized water. As leaching continued, dispersion eventually subsided as Ca for Na exchange resulted in reduced exchangeable sodium percentage. Higher carbon dioxide concentrations of the extractant resulted in increased calcite dissolution and prevented clay dispersion. These results suggest that the dissolution of indigenous calcite alone may be sufficient to significantly change the composition of the soil solution, which results in improving the effectiveness of the soil to resist the negative impact of sodic conditions.