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Citrus is grown globally throughout the subtropics and semi-arid to humid tropics. Abiotic stresses such as soil water deficit negatively affect plant growth, physiology, biochemistry, and anatomy. Herein, we investigated the effect(s) of three water regimes (control, moderate drought, and severe drought) on the physiological and anatomical structure of 10 different citrus rootstocks with different degrees of tolerance to drought stress. Brazilian sour orange and Gadha dahi performed well by avoiding desiccation and maintaining plant growth, plant water status, and biochemical characters, while Rangpur Poona nucellar (C. limonia) and Sunki × bentake were the most sensitive rootstocks at all stress conditions. At severe water stress, the highest root length (24.33 ± 0.58), shoot length (17.00 ± 1.00), root moisture content (57.67 ± 1.53), shoot moisture content (64.59 ± 1.71), and plant water potential (−1.57 ± 0.03) was observed in tolerant genotype, Brazilian sour orange. Likewise, chlorophyll a (2.70 ± 0.06), chlorophyll b (0.87 ± 0.06) and carotenoids (0.69 ± 0.08) were higher in the same genotype. The lowest H₂O₂ content (77.00 ± 1.00) and highest proline content (0.51 ± 0.06) were also recorded by Brazilian sour orange. The tolerance mechanism of tolerant genotypes was elucidated by modification in anatomical structures. Stem anatomy at severe drought, 27.5% increase in epidermal cell thickness, 25.4% in vascular bundle length, 30.5% in xylem thickness, 27.7% in the phloem cell area, 8% in the pith cell area, and 43.4% in cortical thickness were also observed in tolerant genotypes. Likewise, leaf anatomy showed an increase of 27.9% in epidermal cell thickness, 11.4% in vascular bundle length, 21% in xylem thickness, and 15% in phloem cell area in tolerant genotypes compared with sensitive ones. These modifications in tolerant genotypes enabled them to maintain steady nutrient transport while reducing the risk of embolisms, increasing water-flow resistance, and constant transport of nutrients across.