Purpose Partial rootzone drying (PRD) typically alternates the dry and irrigated parts of the rootzone, but how plant physiology and soil evaporation respond to this alternation are poorly understood. Methods Dwarf tomatoes were grown in small split pots comprising two 250 cm3 compartments and fully irrigated (WW: 100% ETc) or subjected to three deficit irrigation treatments (75% ETc): homogeneous rootzone drying (HRD; irrigation evenly distributed); fixed PRD (PRD-F, irrigation applied to one fixed compartment); alternated PRD (PRD-A: as PRD-F but alternating the irrigated compartment every three days). Stem diameter and evapotranspiration were monitored during alternation cycles. The day after alternating the irrigated side of the root system, whole-plant gas exchange and leaf water potential were measured following step increments of vapour pressure deficit. Results Alternation did not affect stem diameter contractions or evapotranspiration, which were lower in HRD than in the two PRD treatments. However, soil evaporation was higher in HRD and PRD-A after alternation than in PRD-F. Following alternation, higher soil evaporation was counteracted by decreased transpiration compared with fixed PRD, despite similar overall soil water content. VPD increments did not change this pattern. Conclusion Irrigation placement determined soil moisture distribution, which in turn affected soil evaporation and whole plant gas exchange. Optimising the frequency of PRD alternation to maximise water savings while ensuring productive water use needs to consider how soil moisture distribution affects both soil evaporation and plant water use.