Study region: Climate change is expected to severely impact Egypt’s Nile Delta Aquifer (NDA). Despite its large freshwater reservoir, estimated at 400 Billion Cubic metres (BCM), climatechange- induced drivers (drought and sea-level rise) coupled with increasing groundwater overabstraction will cause a gradual reduction of the available freshwater volume. This study used the numerical model SEAWAT to study the impact of the main hydrogeological and anthropogenic factors on the response of the submarine groundwater discharge (SGD) (i.e., the net fresh seaward groundwater flux) and seawater intrusion (SWI) in the NDA. Study focus: Five scenarios were examined, including (i) a probable Sea-level rise (SLR), (ii) expected reduction in Nile hydrograph and its branches, (iii) freshwater overpumping, (iv) the combination of reduction in Nile hydrograph and overpumping, and (v) the combination of these scenarios in the years 2030, 2050 and 2070. New hydrological insights for the region: The results show that the increasing saltwater head due to SLR coupled with a reduction in Nile flow and overpumping ultimately results in the landward shifting of the saltwater within the aquifer. In addition, the resulting salinity increase in the aquifer caused a significant increase in the deterioration of a large quantity of freshwater volume with a subsequent reduction of the SGD. Also, the salt mass variation (SMV) in scenario 5 increased to 7.09%, 10.69%, and 12.99%, while the groundwater discharges variation (SGDV) to the sea declined by 21.90%, 42.38%, and 61.95% in the years 2030, 2050 and 2070, respectively. Moreover, the coastal aquifers required the management of the SGD to keep the balance between the freshwater and saltwater interface. This study is useful for the future planning and water resources management in coastal regions for integrated management of SGD, SWI, and aquifer freshwater storage. Also, the applications of smart measurements of SGD and groundwater salinity are required for coastal aquifers management