Evapotranspiration (ET) is an important component of the surface energy and hydrological balance and the main consumptive agriculture water use. Commonly used methodologies to estimate ET require validation with field data to provide accurate results. In addition, the evaluation of the net ecosystem exchange rate (F-NEE) has gained interest in recent times. There is still very little information available about carbon fluxes in citrus orchards. In this study, the eddy covariance (EC) technique was used to determine the actual evapotranspiration (ETe-ec) and the F (NEE) during three irrigated seasons over a flat citrus orchard. Actual seasonal crop coefficients (Kc-ec) were derived by ETe-ec/reference ET. Average ETe-ec for the whole experiment was 1.74 mm/day. Kc-ec showed great variation throughout the year (from 0.40 to 1.20) which was mainly associated with rainfall events. A pronounced variability within both the same season and between seasons was also observed for F-NEE. Based on 2009 data, the only year with a complete database, the citrus orchard acted as a sink for CO2, fixing 3855 kg CO2/ha/year. The results complement previous studies in large lysimeters and provide quantitative information for conducting carbon balance in citrus orchards under Mediterranean conditions.