Shortage of surface water is considered an international problem that has even extended to countries that have rivers, in particular countries sharing the same river basins and downstream countries, such as Egypt. This issue requires intensive management of available water resources. Irrigation Canals Rehabilitation (ICR) has become essential to protect surface water in irrigation canals from losses due to seepage. Egypt is one of the countries that has started using this technique. This paper aims to evaluate the impact of ICR using concrete on the land and on crop yields. The SEEP/W model is used in the current study to estimate changes in the groundwater table and moisture in the root zone. Three cases studies have been simulated and compared including unlined, lined, and lined canals with a drainage pipe. The methodology is applied to three canals in the Nile Delta: Sero, Dafan, and New-Aslogy. The results demonstrate that ICR has decreased the losses from canals which resulted in lowering the groundwater, where the case of lining gave a higher reduction than the case of lining with a drainage pipe. In addition, the water table underneath the embankment was lowered. Decreasing the groundwater table could help to protect the land from logging and increase crop yields, but it may reduce the recharging of groundwater aquifers. Such a study is highly recommended in arid regions to decrease water losses where many countries are suffering from water shortage.