This study examines the relationship between foliar application of two micronutrients, i.e., Fe or Mn (at rates 0, 100, 200, and 300 ppm) and different water stress levels (100% as control, 80 and 60% of ETo) during two seasons of 2022 and 2023. Water stress had a negative effect on growth characteristics and yield composition. Foliar application of Fe and Mn showed a positive effect on plant productivity as well as alleviating water stress. Spraying Fe or Mn (300 ppm for each) at 80% ETo led to increased plant height by 49.80 and 52.54%, number of branches by 52.08 and 65.43%, herb yield 25.40 and 29.38%% and oil yield 36.08 and 30.58%, respectively, compared with non-treated plants. Water stress and micronutrients have a positive effect on the antioxidant activity (DPPH%) of the essential oil. GC-MS analysis of essential oil showed that the monoterpenoid composition of marjoram was affected by water stress level, but the effects may have been indirect via an alteration in development rate. Increasing water stress initiated a reduction of monoterpene or sesquiterpene hydrocarbons and accelerated the transformation of hydrocarbons into oxygenated components.It could be concluded that foliar application of marjoram plants with Fe or Mn at 300 ppm obtained the optimal characteristics of marjoram plants under experimental conditions. On the other hand, to obtain high oil content with high antioxidant activity of essential oil it could be recommended to irrigate marjoram plants with 80% ETo and 300 ppm of Mn as foliar application.