The use of desalinated seawater (DSW) for irrigation in semi-arid regions is taking hold. Citrus tolerance to ions that predominate in DSW and water stress depends on the rootstock. Deficit irrigation was applied to DSW-irrigated lemon trees and grafted on rootstocks with different tolerance (Citrus macrophylla(CM) and sour orange (SO)). Plants were irrigated with DSW or Control treatment (distilled water), and, 140 days later, irrigation treatments were started: full irrigation (FI) or DI (50% of the volume applied to FI). After 75 days, differences between CM and SO plants irrigated with DSW and under DI were found. The higher concentrations of Cl−and Na+in CM and B in SO were the main causes of shoot growth reduction. The osmotic adjustment of CM plants was made possible by the accumulation of Na+, Cl−, and proline, but SO failed to adjust osmotically. In CM and SO plants, photosynthesis reduction was due to lower chlorophyll levels, but also to stomatal factors (CM plants) or alterations of the photochemical machinery (SO plants). Finally, unlike CM, SO had a good antioxidant system. In the future, knowing the different responses of CM and SO under these stressful conditions could be useful in citrus-growing areas.