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Biological activity in semi-arid and arid ecosystems is strongly dependent on rainfall, particularly in summer. A period of favourable rainfall can alter ecosystem carbon balance and is likely influence inner-annual variability of the regional and global carbon cycle. The effect of rainfall variability on ecosystem carbon and water fluxes in semi-arid ecosystems, particularly in woody ecosystems has not been adequately investigated. In this study, we used eddy covariance data from four springs (September November), four summers (December of that year February of the following year) and three following autumns (March May) between 2010 and 2013 in a semi-arid woodland of southern Australia to better understand the effect of pre-summer, summer and post summer rainfall variability on diurnal pattern of carbon flux. In 2010/11 summer, La Nina conditions resulted in extensive rainfall, which marked an historic record over the last 100 years. The 2011/12 summer was also moist. In contrast, the two following summers (2012/13 and 2013/14) were dry. Cumulative net ecosystem productivity (NEP) was lower in dry summers than in moist summers, due to lower maximum carbon flux rate and total hours of net carbon uptake. Maximum NEP and gross primary productivity rates on a given day were reached earlier in dry summers, indicating that photosynthetic activity was not suppressed by high temperatures but by water availability. Ecosystem water use efficiency, calculated as the ratio of daily NEP to evapotranspiration, was higher in moist than dry summers. In addition, the effect of summer rain extended into the following autumn. Cumulative NEP and ecosystem water use efficiency in autumn following a dry summer were lower than when following a moist summer. We conclude that summer rainfall has a strong impact on the carbon cycle in semi-arid woodlands due to its direct and carry-over effect. Therefore seasonal rainfall variation is likely to determine inter-annual variability of annual net carbo uptake of this ecosystem.