In arid and semi-arid regions, irrigation management is important to avoid water loss by soil evaporation and deep percolation (DP). In this context, estimating the irrigation water demand has been investigated by many studies in the Haouz plain. However, DP losses beneath irrigated areas in the plain have not been quantified. To fill the gap, this study evaluated DP over two drip-irrigated citrus orchards (Agafay and Saada) using both water balance and direct fluxmeter measurement methods, and explored the simple FAO-56 approach to optimise irrigation in order to both avoid crop water stress and reduce DP losses in case of non-saline and saline soils. The experimental measurements determined different terms of the water balance by using an Eddy-Covariance system, fluxmeter, soil moisture sensors and a meteorological station. Using the water balance equation and fluxmeter measurements, results showed that about 37% and 45% of supplied water was lost by DP in Saada and Agafay sites, respectively. The main cause of DP losses was the mismatch between irrigation and the real crop water requirement. For Agafay site, it was found that increased over-irrigation had the effect of reducing soil salinity by leaching salts. The applied FAO-56 model suggested an optimal irrigation scheduling by taking into account both rainfall and soil salinity. The recommended irrigations could save about 39% of supplied water in non-saline soil at Saada and from 30% to 47% in saline soil at Agafay.