Water stress is a major environmental factor affecting Citrus spp. and Rangpur lime is a drought-tolerant rootstock used to improve orange yield in rainfed orchards. Aiming a comprehensive spatio-temporal evaluation of citrus responses to drought, we combined morpho-physiological analyses with metabolic profiling of roots and leaves of Valencia orange scions grafted onto Rangpur lime, Swingle citrumelo or Sunki mandarin rootstocks under water deficit. Plant responses were evaluated during the initial phase of reduction in water availability, when water deficit was maximum and after rehydration. Fifty-eight primary metabolites were modulated by water deficit, mainly amino acids, organic acids and sugars. Metabolic changes indicated adjustments related to osmotic, energetic and redox processes under low water availability, which were dependent on rootstock and varied between roots and leaves and along the experimental period. Water deficit induced minor metabolic changes in Swingle citrumelo rootstock, while Sunki mandarin invested more energy in protective compounds. Regarding the drought tolerant rootstock, our data revealed a more advantageous strategy of Rangpur lime when facing water deficit, which combines cell protection through the reinforcement of antioxidant metabolism and the maintenance of energy supply to first improve root growth during water shortage and then shoot growth just after rewatering.