The Annaba region, situated in the northeastern part of Algeria, harbors significant groundwater resources vital for supplying water to the population, agriculture, and industry. However, increasing pressures from heavy water depletion are raising serious concerns. Continuous exploitation of the aquifer has led to deteriorating water quality and adverse effects on its hydrodynamic equilibrium, resulting in saline intrusions that threaten aquifer utilization and wetland functionality. This study aims to investigate the mechanisms of marine intrusion to characterize saline pollution, identifying the key factors and solutions for seawater contamination of aquifers. Projections for 2035, assuming current climatic conditions and exploitation practices, indicate that without intervention, the negative impacts on groundwater and ecosystems could become catastrophic. The saline intrusion is expected to advance inland by 200 to 300 m on the eastern edge, 500 m in the center of the plain, and up to 1500 m further west. Numerical simulation models, considering environmental heterogeneity, have proven highly effective for understanding the hydrodynamic behavior of aquifers. These models also highlight the vulnerability of coastal aquifers to seawater inflows and significant chloride concentration fluxes. To address the urgent problem of increasing water scarcity in Algeria’s coastal plains, several recommendations have been proposed.