Dwarfing rootstocks are used to control tree vigor allowing for increased densities that increase apple production. Although there is considerable variation among rootstocks in dwarfing capacity, the mechanisms by which rootstocks affect vigor in apple scions remains unclear. Here, Honeycrisp apple growth and water relations were compared among three rootstocks; M-9 as the industry standard and two less studied Geneva series rootstocks; G.87 and G. 814 in Washington, USA. Trees were acquired from a commercial nursery and planted in 2017. In 2018 and 2019, scion physiological, isotopic and morphological traits were measured to better understand the link between rootstock-driven vigor and physiological traits. Rootstock affected scion shoot growth (P <0.001), stomatal conductance (P< 0.01) and stem water potential (P <0.001). Rootstocks with low vegetative vigor like M.9 also had lower stomatal conductance and enriched leaf δ13C and δ18O isotope composition. Plant growth was positively correlated with stomatal conductance and stem water potential. Rootstocks also affected plant water status and net gas exchange. Here, we report an association between rootstock-induced vigor and scion physiological traits such as gas exchange, stem water potential, and leaf carbon and oxygen isotope composition. This research has implications for the understanding of the mechanisms of dwarfing by rootstocks in apple.