The response of the carbon and hydrological cycles of irrigated agro-ecosystems in semi-arid regions to changes in temperature and increasing levels of atmospheric carbon dioxide concentrations is unclear. Furthermore, the extent to which these systems contribute to the carbon cycle as net sources or sinks of carbon dioxide remains relatively unknown. In this study, eddy covariance methodologies were employed to quantify mass and energy exchange of maize, rice and wheat grown in an Australian semi-arid irrigation-dependent agricultural region. It was found that there was a distinct seasonal difference in the magnitude of energy balance components. The latent heat exchange observed during the summer growing season was almost twice that observed during winter. Irrigation management practices significantly influenced the distribution of turbulent fluxes. Over the permanently flooded rice crop, the energy balance was predominately driven by latent heat flux, which accounted for *99 % of the energy balance. For the crops irrigated intermittently (i.e. maize and wheat), latent heat flux represented ~80 % of the energy balance. In addition, all three crops acted as a net carbon sink over the growing season. The rate of carbon assimilationwas impacted by the nature of the photosynthetic pathway of the plant and seasonality. Maize, a C4 plant, exhibited the greatest capacity for carbon uptake(-1,327 g C/m2) during the summer months, and winter wheat, a C3 plant, exhibited the least (-388 g C/m2).