The variation of plant functional traits, from the cell to the whole-plant level, is a central question in trait-based ecology with regard to understanding ecological strategies and adaptations that result from environmental drivers. Here, we analyzed whole-plant and leaf traits of the phreatophyte Ziziphus lotus (L.) Lam., a long-lived shrub that dominates one of the few terrestrial groundwater-dependent ecosystems (GDEs) in Mediterranean Basin drylands. We (a) assessed architectural traits and growth patterns, (b) analyzed leaf morpho-functional traits (specific leaf area [SLA] and stomata pore index [SPI]) and physiological traits (gas exchange rates), as well as their variations within individuals, and (c) evaluated temporal variations in modular growth (i.e., sequential iteration of structural units) between growing seasons and in leaf traits within seasons. Z. lotus' growth pattern was based on the repetition of modules composed of shoots (short and long) and branches (flowering and plagiotropic) that promoted a functional differentiation between vegetative and reproductive structures, respectively. We identified morpho-functionally distinct leaves (i.e., heterophylly) borne on different types of branches. Leaves on flowering branches had higher SLA and water use efficiency (WUEi), but lower SPI and transpiration rates than leaves on vegetative ones. We also observed trade-offs in the elongation of vegetative and flowering structures between growing seasons: the shorter the long shoots, the larger the flowering branches. The modular differentiation and heterophylly of Z. lotus might contribute to prioritizing the investment of resources of this phreatophyte, either for growth or reproduction, and could improve the efficiency in uptake and conservation of resources in drylands.