Land subsidence (LS) due to the Sea Level Rise (SLR) and over-pumping was observed in many groundwater aquifers worldwide. The geotechnical properties and numerical simulation are considered a new integrative approach to investigate the LS hazard. This study investigates the environmental hazards related to LS in the quaternary sediments using laboratory and numerical modeling in the coastal aquifer of Nile delta, Egypt, due to SLR and over-pumping. Therefore, the geotechnical tests are conducted for the aquifer cap and classify the surficial soil as silty clay with moderately complex dispersive characteristics. In addition, hydraulic conductivity and one-dimensional consolidation of silty clay samples were analyzed to estimate the long-term settlement. Consequently, the groundwater head and drawdown were simulated for the current situation. Three proposed future scenarios are SLR and increased abstraction using the SEAWAT code. The results show that groundwater heads increased to 5.65, 14.50, and 26.70 cm for 2020, 2040, and 2060, respectively. Moreover, the estimated LS under the over-pumping scenario reached 7.60, 32.40, and 52.70 cm, with a maximum drawdown of 2.10, 9.70, and 15.10 m. SLR and over-pumping induce more inundation in the northern part due to SLR. The shoreline moves inland with a drawdown to 2, 9.50, and 14.80 m. Integration of measured and groundwater simulation settlements would provide appropriate information about the potential environmental hazards. Moreover, the future LS scenarios help stakeholders to make the right decision in developing effective measures in coastal aquifers to minimize the adverse impacts of LS on infrastructure waterways and human life.