Sugar cane is the main source for refined sugar and the sole source for the molasses industry in Egypt. However, it consumes huge amount of water that could be used to produce other high value crops. Sugar beet might be a good alternative to sugar cane. Yet, due to limited water sources in Egypt, it is important to conduct an integrated water management for both crops. Therefore, in this study, water footprint was estimated to enhance water use efficiency and overcome water scarcity problems. Water footprint (WF) and virtual water trade were estimated, during the period from 2012 to 2016, to select the best crop to produce sugar that reduces the gap between production and consumption of sweetens and achieves high income for farmers. Results showed that the average total water footprint for sugar cane and sugar beet were 428.69 and 232.53 m³/ton, respectively. The energetic and economic water productivity for sugar cane were 1354.18 kcal/m³and 1.48 $/m³; while for sugar beet they were 3338.33 kcal/m³and 3.67 $/m³, respectively. Therefore, it is recommended to increase the cultivated area of sugar beet in Egypt. On the other hand, sugar cane had an imported energetic water productivity of 1812.3 kcal/m³ that was lower than the exported one (2304.94 kcal/m³). This suggests that exporting sugar cane is beneficial for Egypt than importing it. However, importing sugar beet is preferable than exporting it because it had a lower exported energetic water productivity (2557.25 kcal/m³) and exported economic water productivity (2.81 $/m³) than imported ones.