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The conventional sub-surface drainage (FD) in the Nile delta clay soil, northern Egypt, results in excessive drainage and low irrigation efficiency (IE). However, a shallower placement of drain might reduce drain outflow and increase IE. The ultimate objective of the present study was to determine the optimum drain depth that minimizes drain outflow and maximizes IE and irrigation water use efficiency (IWUE), while maintaining crop yield and soil salinity. Compared to FD at 120 cm below the soil surface (BSS), the effect of four controlled drain depths (CD) at 40, 60, 80 and 100 cm BSS on drain outflow, IE, salinity buildup, yield and IWUE were investigated for two seasons (2017–18 and 2018–19; wheat-sunflower cropping system). Measurements were conducted for sunflower (as a summer crop). Irrigation was applied based on the soil water content of FD-treatment, thus irrigation depth varied for each treatment. The results showed that decreasing drain depth significantly reduced drain outflow and water input, while IE, seed yield and IWUE were increased. The maximum seed yield and IWUE were obtained at the shallowest drains. Compared with FD at 120 cm, drain depth at 40 cm decreased drain outflow (by 77.20%) and water input (by 29.3%), while increased seed yield and IWUE by 27% and 86%, respectively. Based on water balance, water-uptake from shallow groundwater was maximum for CD-40 cm treatment (31.05% of water-uptake) and was significantly higher than the other treatments. However, by the end of the second season, treatment with drain depth at 40 cm BSS recorded the highest soil salinity (3.6 dS m−1) due to the upward capillary rise of shallow groundwater. Increased soil salinity had no effect on seed yield because it was below the salinity threshold of sunflower. In terms of IE and IWUE, decreasing drain depth to 40 cm BSS is recommended, but with potential salinity buildup. Therefore, drain at 60 cm BSS (had similar seed yield to drain at 40 cm BSS) might lead to significant water-saving (21.8%), while maintaining seed yield and soil quality. In conclusion, modifying the drainage system by reducing drain depth and considering crop water-uptake from shallow groundwater might contribute to water saving. After all, careful water and soil management (e.g., periodic leaching), and suitable cropping systems should be considered for salinity management when decreasing drain depth. • Decreasing drain depth reduced drain outflow and water input and increased irrigation efficiency. • Shallow placement of drain increased seed yield and water use efficiency (WUE) of sunflower. • Shallow placement of drains makes the shallow groundwater available for crop use. • The maximum productivity and WUE were obtained at the shallowest drain depth (40 cm). [ABSTRACT FROM AUTHOR]