Canal seepage losses can contribute significantly to groundwater aquifers in arid and semi-arid regions worldwide. In addition, surface water evaporation and evapotranspiration from adjacent riparian vegetation directly affect surface water availability across these regions. This study aims to evaluate interactions between irrigation canals and the Nile Delta groundwater aquifer in Egypt under four operational scenarios: (i) decreased stream flows in the four main diversion canals associated with upper Nile diversions and climate change, (ii) concrete lining of irrigation canals, (iii) combined lining and use of Photo-Voltaic (PV) Solar Panel covers on canals and (iv) enclosure of the canals in closed conduits. We investigated the effects of these scenarios on regional groundwater supplies and levels using MODFLOW and water budget analyses. Decreased streamflow (scenario 1) resulted in decreased aquifer recharge (from 732 910 to 483 800 m 3 day À1 ) and lower groundwater levels as compared to the base case (present) conditions. Moreover, groundwater flows from the aquifer to the four main canals noticeably increased from 23 176 to 79 364 m 3 day À1 . Water budget analyses associated with canal lining scenarios (2, 3, & 4) indicated that canal leakage to the aquifer accounted for 146 582, 146 582, and 73 291 m 3 day À1 respectively. The changes in canal efficiencies reached 29.3%, 67.1%, 75.3%, and 91.8% while the changes in aquifer recharge efficiencies were 66%, 20%, 20%, and 10% for the four scenarios, respectively. Overall, we found that canals lining is likely the most suitable solution for managing water resources in the Nile Delta. Further aspects to be considered in future studies include the loss of biodiversity along streams embankments due to channel lining.