The rate of metabolic processes demanding energy in tree stems changes in relation with prevailing climatic conditions. Tree water availability can affect stem respiration through impacts on growth, phloem transport or maintenance of diverse cellular processes, but little is known on this topic. Here we monitored seasonal changes in stem CO2 efflux (F-s), radial growth, sap flow and non-structural carbohydrates in trees of Quercus ilex in a Mediterranean forest stand subjected since 2003 to either partial (33%) throughfall exclusion (E) or unchanged throughfall (C). F-s increased exponentially during the day by an effect of temperature, although sap flow attenuated the increase in F-s during the day time. Over the year, F-s also increased exponentially with increasing temperatures, but F-s computed at a standard temperature of 15 degrees C (F-s(15)) varied by almost 4-fold among dates. F-s(15) was the highest after periods of stem growth and decreased as tree water availability decreased, similarly in C and E treatments. The decline in F-s(15) was not linked to a depletion of soluble sugars, which increased when water stress was higher. The proportion of ecosystem respiration attributed to the stems was highest following stem growth (23.3%) and lowest during the peak of drought (6.5%). High within-year variability in F-s(15) makes unadvisable to pool annual data of F-s vs. temperature to model F-s at short time scales (hours to months) in Mediterranean-type forest ecosystems. We demonstrate that water availability is an important factor governing stem CO2 efflux and suggest that trees in Mediterranean environments acclimate to seasonal drought by reducing stem respiration. Stem respiratory rates do not seem to change after a long-term increase in drought intensity, however.