<p>The rehabilitation of irrigation canals may reduce conveyance losses but also diminish recharge to shallow aquifers. One significant source of irrigation canal water loss is seepage. Determining the possible advantages of employing seepage reduction technology and materials requires quantifying the seepage losses in irrigation canals and pinpointing the locations where the seepage loss is most noticeable. However, in numerous regions of the world, seepage from unlined irrigation canals is a major source of groundwater recharge for the shallow aquifers, especially in dry and semi-arid locations like Egypt. The main aim is to assess the effects of canal lining and covering on groundwater recharge and water budget; a secondary aim is to compare numerical seepage estimates with empirical and analytical formulas. In this study, groundwater modeling was implemented utilizing MODFLOW, empirical formulas, and analytical equations were applied. The simulated groundwater level has been compared with the observed groundwater level in observation wells for model calibration. The relationships between Egypt’s central Nile Delta groundwater aquifer system and the irrigation canals in the Gharbia Governorate, considering six operating scenarios: (i) three scenarios of concrete lining of irrigation canals, (ii) three scenarios of covering open canals, (iii) estimate amount of seepage losses from the canals by empirical formulas, analytical equations to verify it with Groundwater Modeling System (GMS) software. The model’s findings demonstrated that the water budget was entirely dependent on the seepage from return flows from irrigated areas, which is the main source of groundwater recharge and supplies roughly 58.4% of the total inflow to the Quaternary aquifer. The seepage from irrigated canals was only a small part of the overall water budget. The leaking from the canal provides around 19.96% of the groundwater replenishment. The percentage of seepage to the canals discharge in the base case (no lining or covering) equaled 2.66%. The concrete lining of irrigation canals (Gharbia and Zefta Directorates canals lining scenario) resulted in a decrease in the aquifer recharge (from 602081 to 23921 m³/day). The percentage of seepage to the canals discharge in this scenario reduced from 2.66% to 0.105 %. The water budget analyses associated with converting the open irrigation canals to covering (Gharbia and Zefta directorates canals covering scenario) showed that the aquifer system’s canal leakage accounted for 0.06 m³/day. The percentage of seepage to the canals discharge in this scenario reduced from 2.66% to 0.0 %. Also, the results showed that the empirical formula, Molesworth &amp; Yennidunia (0.24 x 10⁹) m³/year along with GMS software (0.22 x 10⁹) m³/year, had good agreement with the results. The outcomes demonstrate that improvements in irrigation conveyance efficiency are accompanied by reductions in groundwater aquifer replenishment. Therefore, canal rehabilitation strategies should be evaluated not only in terms of surface-water conservation but also with respect to their impact on groundwater resources. The outcomes of this research could be helped the decision makers and the stakeholders for achievement of proper water resources management and sustainable development goals (Egypt view 2030) in the central Nile Delta, Ghariba Governorate, Egypt.</p>