Stevia (Stevia rebaudiana Bertoni), a perennial crop of the family Asteraceae, is one of the most important sources of non-caloric natural sweeteners, but research on the impact of salinity on root parameters and steviol glycoside content is limited or does not exist. The objective of this study was to assess the effect of exogenous application of iron (Fe), boron (B), and selenium (Se) on root characteristics, growth, and yield of stevia under four levels of NaCl salinity (i.e., 0, 30, 60, and 90 mM). Root length (RL), root volume (RV), root area (RA), and root fresh and dry weight (RFW and RDW) were significantly decreased with increasing salinity. The highest values of all the above root traits were observed with foliar spraying B plus Se plus Fe. Foliar spraying B plus Se plus Fe resulted in 2.9 times greater RV and 2.8 times greater RFW than control. Furthermore, salinity significantly decreased plant height, branches number, leaves number, and biomass yield of stevia. However, foliar application of micronutrients, especially B and Se, reduced those adverse effects. Moreover, salinity decreased the relative water content (RWC) and increased relative water loss (RWL) in stevia tissues. The highest RWC and the lowest RWL were observed in foliar application of B plus Se. Foliar spraying of nutrients significantly improved root characteristics and water status of salt-stressed stevia plants, which in turn (i) helped plants to tolerate excessive Na levels and (ii) improved nutrient uptake under salinity stress. In light of the above, foliar treatment of stevia plants with micronutrients for improving growth under saline conditions could be considered, but toward that direction, studies under field conditions would be required to quantify the efficiency of these micronutrients in foliar applications.