• Drying a portion of a root system (partial root-zone drying (PRD)) can induce partial stomatal closure, but this response is not always observed. We hypothesized that some of the variation in PRD response reflects adaptations to the native environment, where plants subjected to frequent PRD events may display a greater degree of root-level compensation. • Here, we examined PRD responses of Melaleuca argentea, a tree native to intermittent waterways in which PRD events are common. Seedlings were grown with part of their root system in soil and part in an aquatic compartment, mimicking conditions often observed in the field. • The aquatic roots initially provided two-thirds of total water uptake, but draining the aquatic compartment had no effect on stomatal conductance, so long as soil moisture remained c. 80% of field capacity. Water uptake from the soil compartment increased threefold within 24 h, with a corresponding transient threefold increase in root hydraulic conductance (L(p)), an increase in plasma membrane intrinsic protein 1 (PIP1) aquaporins at 24 h, and a decrease in PIP2 aquaporins by 48 h. • Our results demonstrate that PRD can induce rapid changes in L(p) and aquaporin expression in roots, which may play a role in short-term water uptake adjustments, particularly in species adapted to heterogeneous water availability.