The aim of this study was to investigate the effects of magnetized water treatment (MWT) on some vegetation growth indices in arid areas of northeast Iran. For this purpose, the impacts of MWT were examined in terms of leaf area, special leaf area, and some of the physiographic indicators such as relative water capacity and foliar chlorophyll content in three species endemic to arid environments, namely Nitraria, Haloxylon, and Atriplex. In addition to the factors mentioned, acidity (pH) and electrical conductivity (EC) were also measured. This research was conducted in a completely randomized block design with three replications. Data analysis was carried out via the analysis of variance using MSTAT software. The results showed that species irrigated with magnetized water had better performance on measured growth indices. On average, the amount of increase for morphology and physiology parameters in the three species irrigated by MW (comparing with those irrigated by normal water) were: leaf development by 121.74 (19.59%), leaf area index (LAI) by 108.97 (17.5%) mm2, special leaf area (SAL) by 8.68%, relative water content (RWC) by 9.81%, and special product analysis division (SPAD) by 14.77%. The water magnetization process also reduced pH by 0.5 and EC by 0.3 μmhos.cm−1.