While the advantageous effects of using magnetic and electromagnetic treatment (ET) of brackish and saline waters on soil salinity reduction in the root zone were largely reported, more studies are needed to answer questions about the soil salt leaching efficiency and the effect of the duration of the exposure to ET. For this aim, pot experiments were conducted using an Aqua-4DR physical water treatment device. The first experiment included two trials. The first trial considered five concentrations: C0:1.0; C1:4.5; C2:9; C3:13.5; and C4:18 dS m−1. The results revealed that the volume and the salt concentrations of the drained waters were significantly higher under irrigation with ET saline waters than those provided by untreated waters. The drained fraction of water varied from 20 to 26% under irrigation with untreated water and increased from 33 to 56% under irrigation with electro-magnetized water, indicating an improvement in the salt leaching. The second trial was carried out with different irrigation doses. The results showed that the higher the dose, the more obvious and significant the ET effect. The different treatment durations of water exposure revealed that the volume and salinity of drained water significantly increase as the ET duration increases. An increase in the ET duration also induces an increase in the soil water content of around 2.5%. Based on the experimental findings, we may conclude that the ET of saline water can reduce the adverse effect of salinity on the top soil, but these leached salts are carried away in depth and there is no concentration limit of water to the effect of the ET.