Water resources management in high-stress regions is a large-scale problem affecting food and water security. Therefore, modern irrigation systems such as sprinklers, subsurface, and drip irrigations are applied to manage the water shortage in regions of the Nile delta. Because of the increase in population rate and climate change, freshwater supplies are significantly limited and must be efficiently managed. Consequently, Egypt plans to implement MIS in the old land of the Nile delta. The current study aims to investigate and model the recharge from the excess irrigation system that affects groundwater storage and land subsidence unexpectedly. The visual modflow was applied to investigate the groundwater heads and drawdown. At the same time, the analytical solution based on Terzaghi theory, and the surfer software was used to estimate and map the land subsidence. For this reason, we investigated the groundwater drawdown in the high-water shortage of Egypt’s Nile delta. Three scenarios were considered by changing irrigation methods and their Impact on land subsidence in the Nile Delta Aquifer (NDA). Therefore, the results of this study demonstrated that the groundwater drawdown reached 2.60 m, 4.20 m, and 6.50 m, respectively. In contrast, the land subsidence outstretched 26 m, 44 m, and 65 cm for the sprinkle sub-surface. Future design infrastructures such as pipelines, roads, irrigation networks, canals, and water structures should consider land subsidence due to modern irrigation systems (MIS).