Salinity and high boron (B) concentrations are important co-limitations to crop production on naturally occurring alkaline soils in low rainfall regions of the world. Although the interactive effects of salinity and B toxicity on Brassica juncea growth have been reported in slightly acidic soils, very little is known about the interactive effects in alkaline soils. In the current study, a moderately tolerant (Vaibhav) and sensitive (Xinyou5) variety, were grown hydroponically for four weeks to assess mild salinity (50 mM NaCl) with or without high B (1 mM B) at moderate alkalinity (pH 8.5/5 mM NaHCO3). The growth of the two varieties was more affected under the combined treatment than either salinity or high B alone. Although growth rate reduction was similar among the varieties, Vaibhav maintained a lower sodium (Na) and B and a higher potassium (K) concentration in the leaves than Xinyou5. In response to salinity, Vaibhav demonstrated essential tolerance mechanisms of partial exclusion and presumably compartmentalization of Na, leading to greater biomass than Xinyou5. Despite being able to better exclude B, Xinyou5 suffered a greater growth penalty, indicating higher B sensitivity than Vaibhav. In conclusion, screening for individual stresses is not necessarily the best strategy because plant responses to a single stress either salinity or high B may not always be the same as observed when both stresses are present together. Therefore, Brassica germplasm screening is essential for stresses in combination but not separately.