Tetraploid (4x) citrus seedlings may be more tolerant to salt stress than diploid (2x) genotypes. Genome duplication in citrus changes both plant physiology and anatomy, leading plants to acquire differentiated capacities to uptake and transport mineral elements. To provide insight into this behaviour, 2x and 4x Citrus macrophylla (CM), seedlings were grown at moderate (40 mM NaCl) and high salinity (80 mM NaCl) for a period of 30 days. Moderate salinity reduced the biomass of 4x plants, but did not affect the 2x plants, even when diploids accumulated more chloride (Cl−) and sodium (Na+) ions in leaves than tetraploids. The leaf K+ concentration descended in 2xCM leaves but not in the tetraploids. These differences were correlated to variations in uptake and transport rates between the genotypes. Leaf osmotic potential in salinized plants was lower in 2x than in 4x leaves, but water potential and turgor were similar between them. Tetraploid plants had a stronger decrease in their gas exchange parameters than diploids when subjected to moderate salt stress. Leaf damage was only observed in 2x plants subjected to high salinity media, and was correlated with higher Cl− leaf concentration than 4x plants, while Na+ did not differ between them. Taken together, our results suggest that genome duplication improves the tolerance to saline toxicity in CM, because the lower Cl− accumulation in leaves delays the damage. This effect may be linked to the reduced transpiration rate of the 4x genotype.