Agriculture is a major driver of soil salinization/sodification. Specifically, irrigated agricultural lands may face salinization and sodification, resulting in the formation of secondary solonchaks. An on-farm study was conducted in the hyper-arid southern Negev of Israel, where conventional mixed-tree horticultural systems have been irrigated with saline water. Compared with the relatively moderate saline-sodic conditions of nearby natural lands (electric conductivity (EC) = 21.7 +/- 2.4 dS m-1; sodium adsorption ratio (SAR) = 26.8 +/- 4.5), the conventional horticultural systems have faced much greater salinity and sodicity (EC = 85.3 +/- 7.8 dS m-1, and SAR = 50.3 +/- 6.8). However, integration of irrigated cover cropping in some of these systems significantly lowered their saline/sodic levels (EC = 4.6 +/- 0.8 dS m-1, and SAR = 3.2 +/- 0.4). Our analyses show that total organic carbon and labile organic carbon were greatest in soils under the cover cropping (34.4 +/- 3.5 g kg-1 and 1643.7 +/- 115.4 mg kg-1, respectively), intermediate under the conventional horticulture (20.9 +/- 2.1 g kg-1 and 825.6 +/- 151.3 mg kg-1, respectively), and lowest under the natural land (4.2 +/- 0.3 g kg-1 and 41.2 +/- 4.43 mg kg-1, respectively). Soil quality index (SQI) under cover cropping (0.628 +/- 0.015) was 32% and 54% greater, respectively, than that under natural land (0.476 +/- 0.007) and conventional horticulture (0.408 +/- 0.018). The integration of cover crops evidently facilitated a net output of salts from the soil, enabling remediation of the secondary solonchaks. Yet, the specific mechanisms underlying this effect remain unquantified. The increasing global demand for agricultural production, consequently increasing the use of marginal lands and low-quality water sources, makes this study relevant for sustainable development in the future.