•Sodicity was investigated in a semiarid Calcisol of the Great Konya Basin.•pH gradually increased while the EC decreased with irrigation water treatment.•Water quality strongly influenced ion concentrations in calcareous soils.•Short-term leaching with poor-quality waters restricts permeability.•Poor quality irrigation treatments increase the risk of secondary salinization. The often-indispensable use of poor-quality irrigation water in drylands instigates diverse physicochemical dynamics leading to soil salinization and sodicity which are recognized as major contributors to land degradation. This study aimed to examine the effects of water quality and irrigation mode on solute transport conditions in terms of ion exchange of colloidal particles. Laboratory studies with undisturbed soil columns were carried out with two water treatments - tap and sodic waters - as well as two water flow velocities: fast leaching which corresponds to Darcy velocity equal to the saturated hydraulic conductivity and slow leaching equal to half the fast-leaching case. Results indicated that the flow velocities did not significantly influence pH, EC and ion concentrations due to the high calcium carbonate and clay contents of the soil which make the soil less permeable. However, flow velocity rapidly decreased in the fast leaching compared to that in slow leaching as the sodic water was applied. This reveals the destructive effect of Na+ in the soil. The EC rapidly dropped at the beginning of leaching for both water qualities opposite to pH, then became steady. All sodic applications caused an increase in Na+ till the end of treatments. This also resulted in variations in measured soluble anions. In general, sharp decreases in highly soluble anions were observed in all treatments, leading to an increase in HCO3–, especially for sodic treatments. Overall, sodicity caused significant changes in flow dynamics and ion concentrations and created favorable conditions for secondary salinization in this low permeable soil system.