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Drought is considered to be the main environmental factor limiting photo-synthesis (AN) and, consequently, plant growth and yield worldwide. During photosynthesis, the pathway of CO2 from the atmosphere to the site of carboxylation in the chloroplast stroma has two main components: stomatal (gs) and mesophyll (gm) conductances. Both are finite and dynamic, responding to many abiotic factors, therefore reducing CO2 concentration. However, little is known about gm regulation in the short term, where a possible role of aquaporins (AQP) and carbonic anhydrase (CA) has been proposed. Five-year-old olive trees growing in 50 L pots were used to evaluate the acclimation and recovery of AN to drought and subsequent re-watering. Control trees were well-irrigated, while in stressed trees irrigation was withheld for 13 days and then resumed. We made a simultaneous analysis of the genetic expression of two AQP, OePIP1.1 and OePIP2.1, and of CA, on the one hand, and leaf water status, leaf gas exchange and shoot hydraulic conductivity on the other. This is the first time that genetic expression in olive is related to main physiological variables. Two days after withholding irrigation (a.w.i.), the gs and gm values in Stress tress were lower than in Control trees. This limited photosynthesis. Leaf water status decreased from day 4 a.w.i. Midday leaf water potential dropped from -1.2 on the day before withholding irrigation to -6.0 MPa on day 9 a.w.i. CA expression decreased during drought and there was a peak on OePIP1.1 expression on day 4 a.w.i. Leaf water status recovered in ca. 36 h after resuming irrigation. Both gm and AN did not fully recover until 46 days after rewatering. Stomatal conductance, however, did not recover in that period, probably because of an irreversible loss of shoot hydraulic conductivity. Both OePIP1.1 and OePIP2.1 peaked 36 h after rewatering. We found significant correlations between gm and both OePIP2.1 and CA expression.