The present study concerns the effects of different magnetically treated waters, using distilled water as control, domestic water, saline water (-3 MPa), wastewater and purified water of Arak city; on emergence and growth of Medicago scutellata (Var. Rabinson) seedlings in greenhouse conditions. The various waters were treated by a magnetic field of 250 mT at flow rate of 2 l/min. One hundred seeds per treatment were soaked in magnetically treated waters for 12 hours and cultivated in pots with sand bed. A daily number of emerged seedlings was counted in a daily basis, whereas growth data was measured on the 20th day after planting. Seedlings from seeds exposed to magnetically treated waters showed an improvement of 5-10 percent in the emergence and a 5-14 and 2-16 percent increase in root length and weight, respectively. The values of seedling lengths and dry weight of emerged seedlings in magnetically treated pots, compared with those in untreated pots, showed an increased for distilled water (14.82 and 14.4%), domestic water (14.67 and 16.3%), saline water (13.75 and 9.18%), and purified water (14.04 and 2.92%), respectively. From a practical point of view, it was found that the use of this method is appropriate for improving the agricultural products.