The present study concerns the effects of different magnetically treated waters (distilled water (as control), domestic water, saline water (-3 MPa), waste water and purified water of Arak city) on emergence and growth of Medicago scutellata (Var. Rabinson) seedlings under greenhouse conditions. The various waters were treated by passing it through 250 mT magnetic fields at flow rate of 2 lit/min. One hundred seeds per treatment were soaked in magnetically-treated waters for 12 hours and cultivated in pots with sand bed. The number of seedlings emerged was counted on daily basis, whereas growth data was measured on the 20th day after planting. Seedlings from exposed seeds 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. Dry weight of emerged seedlings in pots by magnetically-treated waters, in comparison with those in untreated pots (control) increased for distilled water (14.4%), domestic water (16.3%), saline water (9.18%), and purified water (2.92%). The results of seedling lengths in the pots of magnetically-treated waters showed that, 5.54, 14.82, 14.67, 13.75, and 14.04 percent increased, respectively. From a practical point of view, it was concluded that could be a promising technique for agricultural improvements.