Composite trees combine traits from both the rootstock and scion. Dwarfing rootstocks are used to reduce shoot vigor and improve fruit quality and productivity. Although differences in rootstock vigour have been clearly described, the underlying physiological mechanisms regulating scion vigor are not well understood. Plant water status is strongly influenced by stem hydraulic resistance to water movement. In the scion, stomata regulate transpiration rates and are essential to prevent hydraulic failure. Lower stomatal conductance contributes to enriched leaf carbon isotope composition (δ13C). Combined, the effects of increased hydraulic resistance, limited stomatal control, and subsequently, limited gas exchange can affect tree growth. These differences may also correspond to differences in scion vigor. Here, vegetative growth, gas exchange, stem water potential, and leaf δ13C were compared to determine how rootstocks affect scion water relations. B.9 had the lowest shoot vigor compared to the more vigorous rootstock, G.890. Similarly, photosynthetic rates were also lower. Rootstock vigor was closely associated with leaf gas exchange and stem water potential in the scion and were reflected in leaf δ13C signatures. Dwarfing was strongly related to hydraulic limitations induced by rootstock genotype and these changes are distinguishable when measuring leaf and stem δ13C composition.