In coastal groundwater aquifers, seawater intrusion is seen as a significant issue. Increasing the groundwater pumping rate enhances seawater intrusion into groundwater in the coastal aquifers. In Egypt, the Nile Delta aquifer (NDA) is extremely vulnerable to Mediterranean Sea seawater intrusion. The study's major goal was to create a three-dimensional groundwater model that included all branches of the irrigation system and their groundwater recharges into the NDA. The NDA model was built by using the SEAWAT program. The model validation was achieved by comparing its results with the observation data and results from previous models. Three scenarios were proposed considering: 1) sea level rise, 2) changes in the rate of groundwater abstraction, and 3) a combination of the conditions of the two previous scenarios' conditions. A rise in Mediterranean Sea levels by 25, 50, 75 and 100 cm caused additional saltwater intrusion to distances of 5.11 km, 7.10, 7.62 and 8.2 km, respectively. Moreover, in comparison to the base situation, a decrease in the lower boundary's groundwater head by 25, 50, 75 and 100 cm caused the saltwater to advance further inland to distances of 5.30, 5.47, 5.52 and 5.75 km, respectively. The third scenario proved to be the worst case, in which saltwater intrusion increased to a distance of 7.22, 7.73, 8.20 and 10.20 km, respectively. Compared with previous model studies, the results showed that saltwater intrusion length decreases by 4.0 km after including all branches of the irrigation network.