The government’s efforts are looking to expand their reclaimed lands however; the major challenges are the sacristy of valid irrigation water availability. Moreover, salinity stress is a major environmental constraint that significantly reduces agricultural productivity worldwide as it forms a harmful effect as a thin layer that interferes with the soil characteristics and prevents seedling growth. While, fennel, is a moderately tolerant plant to salinity exhibits reduced growth and yield under prolonged saline conditions. The current study demonstrates that, salinity stress negatively impacts fennel growth and yield, meanwhile, saline water stress can be mitigated by Magnetic Water Treatment (MWT) at different salinity levels (0.7, 2.5, 4.5, 5.5, 7.5 ds/m). Major effect was noted at salinity levels up to 2.5 and 4.5 ds/m. Morphologically, results reveal that, MWT exerts a significant positive impact on fennel growth and yield throughout the two growing seasons (2020/2021 and 2021/2022) /under saline water irrigation. Nutrients content i.e. chlorophyll a, chlorophyll b, chlorophyll a + b, nitrogen (%), phosphorus (%), potassium (%), and proline (mM) values are all significantly higher after MWT. Finally, the values for bulb dry weight (%) and leaf dry weight (%) are reversed between the two cases. These findings suggest that, MWT is a sustainable approach to enhance fennel growth and yield under saline water stress conditions. MWT practice can be applied to fennel cultivation to improve productivity and reduce the negative effects of salinity. MWT is a promising eco-friendly treatment for saline irrigation water, enabling us to avoid the harmful effects of chemical fertilizers and pesticide pollution.