Current climatic upheavals reduce water availability which impacts the growth and fruit quality of plants. In citrus crops, scion/rootstock combinations are used to ensure high fruit production and quality and a stress tolerance/resistance. Our objective was to assess the effect on the clementine scion (C) under natural mild water deficit of (i) polyploid rootstocks by comparing the allotetraploid FlhorAG1 (C/4xFLs; trifoliate orange + Willowleaf mandarin) with its diploid parents, trifoliate orange (C/2xTOs), and Willowleaf mandarin (C/2xWLs), and with a diploid genotype used as reference (Carrizo citrange, C/2xCCs), (ii) rootstock propagation methods by comparing trifoliate orange seedling (C/2xTOs) with cutting (C/2xTOc). A mild water deficit observed under orchard conditions during the summer period (July–August) induced a significant change in yield (except in C/2xTOs), fruit size, and quality. C/2xCCs, C/2xTOs, and C/2xWLs appeared less affected by water deficit as indicated by their lower reduction of predawn leaf water potential (Ψpd), relative water content (RWC), transpiration (E), and photosynthetic parameters (Pnet and gs). Their greater redox balance was probably due to their better antioxidant efficiency. Seedling rootstocks lead to a better adaptation of clementine scions to water deficit than cutting or allotetraploid rootstock. Improving the tolerance to water deficit requires taking into consideration the rootstock genotype, propagation method, and ploidy level.