Study region The Nile Delta region consists of flat, low-lying areas, where most areas are used for agriculture. It covers an area of 22,000 km2, which is 2.20% of the total area of Egypt. Study focus This study evaluates the water budget and the salinity due to the Sea Level Rise (SLR) and the reduction in the river water flow caused by the Grand Ethiopian Renaissance Dam (GERD) using the numerical code SEAWAT. Three filling scenarios were considered for the GERD reservoir at elevations 600 m, 621 m, and 645 m above mean sea level (AMSL) for the storage volumes of 17 billion cubic meters (BCM) (scenarios #1), 37.30 BCM (scenarios #2), and 74 BCM (scenarios #3). The impact of these fillings scenarios was combined with SLR of 25 cm, and increasing the abstraction rates from the Nile Delta aquifer by 25%, 50%, and 100%, respectively. New hydrological insights for the region The study findings indicated that the SLR and the GERD reservoir filling with increasing pumping rates, especially during the filling periods, would influence the groundwater resources in the Nile Delta. The GERD reservoir filling could alter the freshwater, in which the aquifer salinity increased by 4.47%, 11.48%, and 29.99% for the three scenarios, respectively. The methodology and findings presented in this study might be useful for investing and comparing the impact of SLR and upstream dam projects on the downstream water budget and salinity at other coastal regions.