A study was conducted to investigate the morphological, physiobiochemical, enzymatic, and ionic differences among four cultivated citrus (Citrus sp.) rootstocks with different salt tolerances. Two salt-tolerant rootstocks [Rangpur lime (C. limonia) and Rubidoux (C. trifoliata)] and two salt-sensitive rootstocks [Carrizo citrange (Citrus sinensis × C. trifoliata) and Sanchton citrumello (C. trifoliata × C. paradisi)], were subjected to NaCl stress in greenhouse conditions. The 9-month-old plants were exposed to four different NaCl levels (0, 30, 60, or 90 mm) in sand culture for 3 months. Plant biomass (fresh weight, dry weight, root length, shoot length, and leaf thickness), physiological attributes [number of stomata, stomatal size, number of epidermal cells, photosynthesis rate, stomatal conductance (g S), water use efficiency, and transpiration rate]. and ion content (Na+, K+, Ca+2, Mg+2, and Cl–) were adversely affected by salt stress, but salt-tolerant cultivars were comparatively less affected. Salt stress also enhanced antioxidant enzyme activity (superoxide dismutase, catalase, and peroxidase), particularly in salt-tolerant cultivars. The salt-sensitive cultivars accumulated the greatest content of Na+ and Cl– in their leaves, whereas the salt-tolerant cultivars accumulated the greatest content of Na+ and Cl– in their roots, an adaptation to combat the highly saline conditions. Overall, it was concluded that the salt tolerance of rootstocks is associated with a greater antioxidant enzyme activity and differing accumulation patterns of Na+, K+, Cl–, Mg+2, and Ca+2 in leaves and roots; these can be considered potential indicators of a cultivar's sensitivity to salt stress.