The deleterious effects of sodium-induced secondary alkalinization on soil structure and hydraulic properties of calcareous soils can vary widely. This study aims to evaluate the impact of sodicity and leaching velocity on the physical and hydraulic properties of a calcareous clay-rich soil. Two application rates of tap water (TW) and sodic water (SW) are considered: fast leaching, equal to the saturated hydraulic conductivity, Ks, and slow leaching conditions, equal to have 1/2 Ks. For the TW and SW experiments, up to 14 and 26 leaching cycles were performed in duplicates, respectively. After the leaching applications, the PVC columns were cut horizontally, and undisturbed samples were removed from the different depths. It was observed that neither water quality nor water flow rate significantly affected water stable aggregate percentages. TW did not affect soil total porosity and bulk density except at the bottom of the column. On the other hand, there were remarkable reductions in soil porosity and bulk density in the SW leaching experiments ranging from 8.8 to 12.5% and 7.4–13.8%, respectively. High Na concentrations in leaching water caused aggregate swelling and dispersion, leading to reduced Na+ and enhanced Ca2+ transport to the lower portions of the soil column. In the lower layers, the severity of sodium-induced dispersion was restricted by calcium, which was exchanged by the excess amount of Na from the upper layers, maintaining soil particles flocculated. Ca2+, which tightens the soil particles and aggregates together, limited Na-induced disruption of the soil aggregation. Nonetheless, particles that broke away from aggregate did influence the hydraulic properties of the soils. Overall, the experiments revealed that although the physical and hydraulic properties of the soil are affected by the sodic waters and the flow rates, this effect is reduced in calcareous soils due to their strong bonding feature. •Deleterious effect of Na on aggregation is less evident in calcareous clay-rich soil.•Sodium-induced degradation is more pronounced in the upper layers of calcareous soil.•Aggregates of well-structured calcareous soils resist compaction caused by Na.•Increased flow rates of sodic water accelerate soil degradation.•The higher the limestone and clay content, the more stable the soil structure.