Purpose: Soil sodification through irrigation with alkali groundwater is quite extensive in arid to semi-arid regions of the world. Therefore, the long-term effects of alkali and partially neutralized water irrigations were quantified on sandy loam soils. Methods: The experiment was conducted in semi-controlled concrete lysimeters of 2 × 2 × 2 m3with drainage outlets at bottom and filled with sandy loam soils. These were irrigated with five types of irrigation water, i.e. good quality water (GQW), synthetic alkali water (SAW) having the residual sodium carbonate (RSC) ~ 5 me L−1(SAW1), SAW of RSC ~ 10 me L−1(SAW2), SAW2partially neutralized up to RSC ~ 5 me L−1with gypsum (SAW2+ GYP) and SAW2partially neutralized up to RSC ~ 5 me L−1with sulphuric acid (SAW2+ SA). Results: Perpetual irrigation with residual alkalinity water deteriorated soil quality through increasing its soil pH, electrical conductivity and total inorganic carbon content and diminishing soil microbial activities, total organic carbon (TOC) and its active pools. Increased soil pH further induced negative effect on soil microbial activities and TOC as well as its active pool. Conversely, availability of phosphorous and potassium increased but nitrogen availability remained unaffected. Conclusions: Irrigation with increasing RSC water caused proportionate deterioration in soil quality. Partial neutralization of irrigation water RSC from ~ 10 to ~ 5 me L−1with gypsum or sulphurous amendments did not suffice for sustaining long-term soil quality. It suggested substantial revision in existing recommendation of alkali water neutralization for irrigation to achieve the land degradation neutrality, food security and sustainability.