Water stress (WS) generates a number of physiological and morphological responses in plants that depend on the intensity and duration of stress as well as the plant species and development stage. In perennial plants, WS may affect plant development through cumulative effects that modify plant functions, architecture and production over time. Plant architecture depends on the fate of the terminal and axillary buds that can give rise, in the particular case of apple, to reproductive or vegetative growth units (GUs) of different lengths. In this study, the impact of long-term WS (7 years) on the fate of terminal and axillary buds was investigated in relation to flowering occurrence and production pattern (biennial vs regular) in the ‘Granny Smith’ cultivar. It was observed that WS decreased the total number of GUs per branch, regardless of their type. Conversely, WS did not modify the timing of the two successive developmental phases characterized by the production of long and medium GUs and an alternation of floral GUs over time, respectively. The analysis of GU successions over time using a variable-order Markov chain that included both the effects of the predecessor and water treatment revealed that WS reduced the transition towards long and medium GUs and increased the transition toward floral, short and dead GUs. WS also slightly increased the proportion of axillary floral GUs. The higher relative frequency of floral GUs compared with vegetative ones reduced the tendency to biennial bearing under WS. The accelerated ontogenetic trend observed under WS suggests lower vegetative growth that could, in turn, be beneficial to floral induction and fruit set.