Degradation of soils due to sodification is now widespread in arid and semiarid areas irrigated with groundwater having residual alkalinity. We monitored the changes in soil physical, chemical, and hydraulic characteristics of a sandy loam soil irrigated for the last two decades with two types of alkali waters (AW1, AW2) having similar salts (total electrolyte concentration, TEC=30 me L−1) and sodium adsorption ratio (SARiw 10 mmol L−1) but varying in residual sodium carbonate, RSC (5 me L−1 in AW1 and 10 me L−1 in AW2), and when latter irrigation water (AW2) was ameliorated to neutralize RSC equivalent to 5 me L−1 with either sulfuric acid (AW2 +SA) or gypsum (AW2 +GYP). Deterioration of overall soil quality was evidenced by increased bulk density and penetration resistance, decreased aggregate stability, increased soil pH and sodicity, and decline in accumulation of soil organic carbon, especially with AW2. Exchangeable sodium percentage (ESP) build up ranged between 2.1 and 3.3 times SARiw. The steady infiltration rate (IR) in soil irrigated with good quality water, GQW (Electrical conductivity, ECiw=0.52dSm−1; RSC=1.2 me L−1), was 5.4 mm h−1 (IR-GQW) while it reduced to 2.2, 1.0, 1.7, and 1.8 mm h−1 with AW1, AW2, AW2 +SA, and AW2 +GYP, respectively. The adverse effects of soil sodification exacerbated with rainwater (RW; simulated with deionized water, EC <0.03dSm−1) infiltration, further reducing the IR to 1.1, 0.7, 1.4, and 1.0 mm h−1 for AW1, AW2, AW2 +SA, and AW2 +GYP, respectively. The recovery of IR was only a little (2–11%) when RW was replaced with respective irrigation waters, even when the surface 5 cm was tilled to break soil crusts (ST). This indicates permanent damage to soil structure and water transmission characteristics through the development of sub-soil throttles with moved-in clays. Power functions described the surface soil ESP to control IR (R2 =0.53–0.83 **), and the ESP values for 0.25 IR-GQW were 24.5, 15.8, 17.4, 14.5 and 14.4 for IW (respective irrigation waters), RW, IW-RW, RW-IW, and RW-IW-ST-IW sequences of infiltration events, respectively. There were considerable reductions in post-infiltration water storage in the soil profile, and a slowed down redistribution of infiltrated water were also observed. The neutralization of RSC with either sulfuric acid or gypsum improved the hydro-physical properties; the impact of gypsum being slightly better especially in improving soil stability characteristics.