Apple is a commercially important fruit produced in Iran but due to water scarcity most of the orchards are irrigated with saline waters in arid and semi-arid regions of the country. Recent studies show that magnetization of irrigation water may decrease the adverse effects of salinity on some plants. In order to study the responses of apple seedlings to magnetization of saline water the M7 and MM106 saplings grafted on Golden Delicious rootstock were irrigated with saline water of 0, 40 and 80 mM NaCl exposed to a magnetic field 0, 0.1 0.2 Tesla. Saline water increased the Na+ content of the roots and leaves, hydrogen peroxide and electrolyte leakage of the cells, and decreased the quantum yield, K+ and Ca2+ contents of the root and leaf, relative water content and SPAD index of the saplings. However, the proline, soluble sugars, and phenolics contents, and the activity of catalase, peroxidase, superoxide dismutase and polyphenol oxidase enzymes were increased in saplings irrigated with magnetic water by 70.1%, 105.76%, 72.18%, 183.74%, 107.31%, 11.22% and 104.42%, respectively. Furthermore, all of these parameters were significantly enhanced in response to irrigation with a magnetized non-saline water. Both cultivars showed similar responses to magnetic field treatment. Our results demonstrate that magnetic field exposure ameliorates the adverse effects of saline water by enhancing plant antioxidant systems, water absorbance capacity, photosynthetic activity and absorbance rate of K+ and Ca2+ while decreasing the absorbance rate of Na+. The best results for magnetization treatment were obtained with 0.2 Tesla.