We investigated responses of plant growth rate, hydraulic resistance, and xylem cavitation in scion-rootstock-combinations of Malus domestica L. cv. Honeycrisp scions grafted onto a high-shoot vigor (HSV) rootstock, (semi-dwarfing Malling111), or onto a low-shoot vigor (LSV) rootstock, (dwarfing Budagovsky 9), in response to substrate moisture limitation. Adjustments in xylem vessel diameter and frequency were related to hydraulic resistance measurements for high- versus low- vigor apple trees. We observed a greater tolerance to water deficit in the high-shoot compared to the low-shoot vigor plants under water deficit as evidenced by increased growth in several plant organs, and greater scion anatomical response to limited water availability with ca. 25% increased vessel frequency and ca. 28% narrower current season xylem ring width. Whereas water limitation resulted in greater graft union hydraulic resistance of high-shoot vigor trees, the opposite was true when water was not limiting. The graft union of the low-shoot vigor rootstock exhibited higher hydraulic resistance under well-watered conditions. Scions of high-shoot vigor rootstocks had fewer embolisms at low plant water status compared to scions of low-shoot vigor rootstocks, presumably as a result of large differences in xylem vessel diameter. Our results demonstrated that anatomical differences were related to shifts in hydraulic conductivity and cavitation events, a direct result of grafting, under limited soil water.