<p>Efficient management of irrigation water is critical for sustaining agriculture in the Nile Delta, where canal seepage serves as both a loss from surface water delivery and a key recharge mechanism for the shallow aquifer. This study assessed the impacts of canal lining on groundwater dynamics in Qalubiya and Sharqiya governorates by combining intensive field monitoring with numerical groundwater modeling. A network of 36 observation wells was installed along two lined canals (El-Makasser and El-Zaree) and two unlined canals (El-Wedn and Nabteet). Ninety-seven monitoring campaigns were conducted between May 2024 and June 2025 under alternating canal operation schedules. Unlike previous studies, this research provides field-scale validation of groundwater responses to canal lining under real operational conditions. Results show that groundwater fluctuations in unlined canals were strongly correlated with canal stages, particularly where clay layers were thin, while lined canals showed weaker interactions and greater drawdowns in heavily pumped areas. A MODFLOW-6 model, calibrated with field data (R² = 0.99), simulated two scenarios: lining El-Wedn Canal alone and lining all branch canals. Lining a single canal caused a moderate 0.6 m drawdown after 20 years, while lining the entire canal network produced a widespread 3.5 m decline in groundwater levels. The findings demonstrate that while lining enhances surface water conveyance, it reduces aquifer recharge and may threaten groundwater sustainability. A balanced approach that accounts for local hydrogeological conditions is therefore essential to align canal rehabilitation with groundwater management objectives.</p>