Baobab trees (Adansonia, Bombacaceae) are widely thought to store water in their stems for use when water availability is low. We tested this hypothesis by assessing the role of stored water during the dry season in three baobab species in Madagascar. In the dry season, leaves are present only during and after leaf flush. We quantified the relative contributions of stem and soil water during this period through measures of stem water content, sap flow and stomatal conductance. Rates of sap flow at the base of the trunk were near zero, indicating that leaf flushing was almost entirely dependent on stem water. Stem water content declined by up to 12% during this period, yet stomatal conductance and branch sap flow rates remained very low. Stem water reserves were used to support new leaf growth and cuticular transpiration, but not to support stomatal opening before the rainy season. Stomatal opening coincided with the onset of sap flow at the base of the trunk and occurred only after significant rainfall.