Plant response to drought is a critical process for the survival and development of resilient cropping systems. However, drought studies are often based on short-term experiments under controlled environments which may not reflect compounding stress factors experiences under field conditions, such as high air and soil temperature, high light irradiance, among others. In composite plants like apple, both rootstock and scion combine to modulate drought response. Nonetheless, the effect that apple rootstock genotypes have on scion response to water limitations have not been extensively studied. The objective of this study was to measure physiological responses of different apple rootstocks to drought under both field and greenhouse conditions. For both experiments, ‘Honeycrisp’ apple was grafted onto G.41, G.890, M.9, and B.9 rootstocks. Two irrigation treatments were established: drought (~ 50% of field capacity (FC) and control (~ 100% FC). Leaf gas exchange, mid-day stem water potential (Ψmd), quantum yield of PSII (ΦII) and shoot growth were measured bi-weekly. At the end of each experiment, total leaf area and root, stem and leaf carbon isotope composition (δ13C) were measured. In the field, ‘Honeycrisp’ that was grafted onto G8.90 and exposed to water limitations had lower stomatal conductance, net CO2 exchange rates, ΦII, and shoot growth. In contrast, B.9 maintained stomatal conductance and shoot growth when water-limited and δ13C was the highest among rootstocks. There were no rootstocks differences for trees grown in the greenhouse. These results show how rootstock can affect scion response to water limitations in apple and how field experiments can magnify these responses.