‘Honeycrisp’ apple is susceptible to bitter pit, which is associated with fruit mineral nutrient composition. Rootstock genotypes can affect nutrient acquisition, distribution, and fruit yields, which all affect fruit nutrient composition and bitter pit susceptibility. However, the changes of these traits among different rootstock genotypes in response to abiotic stress under semiarid conditions are relatively unknown. The objective of this study was to evaluate the influence of different rootstocks and irrigation on nutrient uptake and partitioning with ‘Honeycrisp’ apple grown in an irrigated, semiarid environment. ‘Honeycrisp’ apple trees were grafted on four different rootstocks, Geneva 41 (‘G.41’), Geneva 890 (‘G.890’), M.9-T337 (‘M.9’), and Budagovsky 9 (‘B.9’), and these were planted at high density (3000 trees/ha). Irrigation was applied as either a water-limited treatment where volumetric soil water content was maintained near 50% field capacity (FC) and a well-watered control where soil water content was maintained near 100% FC. ‘G.890’, the most vigorous rootstock, had lower nitrogen and higher potassium content in leaves, while ‘B.9’, the least vigorous rootstock, had lower potassium and higher nitrogen content. Rootstock genotype did not affect calcium uptake. Interestingly, water-limited conditions increased the nutrient content in root and stems but not in leaves. Water-limited trees partitioned more nitrogen and calcium to roots, while well-watered trees in the control partitioned more nutrients to the stems. Fruit size was the largest for ‘G.890’ and smallest for ‘B.9’. Both ‘G.41’ and ‘G.890’ had higher bitter pit incidence, which was associated with higher potassium content in leaves and fruit. These results suggest that rootstock-induced vigor and irrigation can both contribute to nutrient imbalances in leaves and fruit that could affect the development of physiological disorders in ‘Honeycrisp’ apple.