As grapevine production is converting into irrigated systems worldwide, understanding rootstock-scion interactions at different stages of moderate drought can help to better manage water resources and the choice of rootstock. This study compared the physio-morphological drought response and recovery of a drought-sensitive (Riparia Gloire (Vitis riparia)) and a drought-tolerant rootstock (Ramsey (Vitis champinii)) grafted with Cabernet Sauvignon (Vitis vinifera), and the self-grafted control in a pot study. Ramsey had lower root-to-shoot ratio but higher performance of the root system under drought, explained by the lower root tissue density and tip suberization and higher VviPIP2;1 aquaporin expression, and faster recovery of root hydraulic conductivity and stomatal conductance after re-watering than Riparia. Riparia maintained better water status under moderate drought by early root suberization, but it was less able to restore water uptake capacity and support scion growth and leaf gas exchange after re-watering. This study shows a suite of rootstock traits that improve scion growth in response to moderate drought. Thus, these results identify traits for breeding programs and the selection of rootstocks for sustainable management of water resources under irrigated production.