ABSTRACT The Nile Delta aquifer stands as Egypt’s second primary freshwater source following the Nile River. Its replenishment deriveed from various sources, including the Nile branches, the surface irrigation networks, and the infiltration of excess irrigation water. The expanded demand for irrigation water causes water shortages at the canal tails of some irrigation canals across Egypt. Farmers have resorted to addressing this issue by illegally excavating shallow wells, employing them in times when surface water is inaccessible. Among the national action plans to improve water availability at canal tails is the lining of distributary canals. However, this intervention potentially obstructs the natural replenishment source of the Nile Delta aquifer, consequently contributing to the deterioration of groundwater quality. Hence, this research aims to evaluate the impacts of lining distributary canals on groundwater status through numerical modeling. Utilizing the MODFLOW package, the study determines the natural infiltration rates from the canals into the adjoining groundwater system. Two prevalent hydrological conditions in Egypt were selected for numerical modeling. The first case study focuses on a Canal, located in Qalyoubia governorate, represents the semi-confined aquifer conditions prevalent in the Nile Delta. The second case study is a Canal, situated in Sharqia governorate, represents the phreatic aquifer conditions present in the Nile Delta. Piezometers were implemented to determine the groundwater levels and for the calibration process. The calibrated models were employed to simulate the expected impacts of canal lining for each case and contrasted with pre-lining infiltration rates. Findings indicate that while canal lining effectively reduces water seepage into shallow groundwater in sandy soils, it is of little avail in clayey top soils. The research recommends implementing integrated water resource management to mitigate the possible impacts of lining. It also suggests prioritizing regular maintenance practices for canal linings, especially in areas with sandy soils.