Developing new tools for using low-quality irrigation waters is vital for the sustainability of irrigated agriculture and minimizing salt accumulation. Therefore, the present study focused on the interactive influence of irrigation treatments (magnetized (MT) and non-magnetized (NMT)) and water salinities (0.38, 1.5, 4.5, and 7.0 dSm−1) on soil salinity, water use efficiency, yield and morpho-physiological changes of Balkız bean. A pot experiment was conducted in a randomized complete block design with three replications under the rain shelter condition. Irrigation water MT treatment increased fresh bean yield, water use efficiency (WUE) and irrigation water use efficiency (IWUE) by 21.35, 23.00 and 14.8%, respectively, while saturated soil salinity was reduced by 20%, compared to NMT treatments. The leaf area, stomata, and leaf succulence in green beans in the MT treatment significantly increased by 13.4, 23.9, and 3.3% compared with those in the NMT treatment. Stems of the bean crops were more sensitive to salinity stress followed by roots and leaves. The study revealed that irrigation with magnetically treated water manages salinity related yield loss through increased morphological features as well as osmotic and stomatal adjustments. In addition, the bean crops showed an ability to protect water in tissue against salinity toxicity up to 5.24 dSm−1 soil salinity level under magnetized saline water conditions. Finally, irrigation with magnetically treated 0.38 dSm−1 irrigation water can be recommended due to providing a higher yield, WUE, IWUE, and sustainable production under saline irrigation in water scarcity regions.