A hydroponic experiment was carried out to investigate the effects of magnetic water irrigation on the growth, nutritional status and antioxidant enzyme activity of cotton seedlings. Four levels of magnetic-treated water irrigation (0, 100, 300 and 500 mT) and three levels of salt stress (0, 100 and 200 mM NaCl) were applied. Salt stress adversely affected the dry weight, nutrient uptake and antioxidant enzyme activities of cotton seedlings. Magnetic-treated water irrigation significantly increased cotton seedling dry weight. Cotton seedling dry weight increased by 14%, 22% and 29% under the treatments of 100, 300 and 500 mT magnetic water irrigation, respectively, compared with the control, at a salt stress level of 100 mM NaCl. Moreover, magnetic water irrigation improved N uptake, but did not significantly affect P and K uptake. Magnetic water irrigation significantly increased the activity of superoxide dismutase (SOD), peroxidase (POD) and the proline content compared to the control (0 mT). Irrigation with magnetic water could be a promising technique in agriculture, especially under salt stress conditions. A suitable magnetic intensity of 300 mT is recommended.