There is a strong need for long term observations of land surface fluxes such as actual evapotranspiration (ETa). Eddy covariance (EC) method is widely used to provide ETa measurements, and several gap-filling methods have been proposed to complete inherent missing data. However, implementing gap-filling methods is questionable for EC time series collected within hilly agricultural areas at the watershed extent. Indeed, changes in wind direction induce changes in airflow inclination and footprint, and therefore possibly induce changes in the relationships on which rely gap-filling methods. This study aimed to obtain continuous ETa time series by adapting gap-filling methods to the particular conditions abovementioned. The experiment took place within an agricultural watershed in north-eastern Tunisia. A 9.6-m-high EC flux tower has been operating close to the watershed center since 2010. The sensible and latent heat fluxes data collected from 2010 to 2013 were quality controlled, and the REddyProc software was used to fill gaps at the hourly timescale. Adapting REddyProc method consisted of splitting the dataset according to wind direction, which improved the flux data at the hourly timescale, but not at the daily and monthly timescales. Finally, complete time series permitted to analyze seasonal and inter-annual variability of ETa.