About 40% of the global population lives in coastal cities, a number expected to rise. Coastal aquifers are vital reserves, especially in arid regions, crucial during droughts. However, human and climatic pressures impact their quantity and quality. Underground infrastructure, like railway tunnels, alters groundwater flow. Retaining walls and drainage systems disrupt flow, reducing water availability and accelerating saline intrusion. Inner docks shift the coastline, worsening the situation. This study analyzes the impact of railway tunnels and an inner dock on the Llobregat Delta aquifer (Spain) from 1966 to 2024. A conceptual and geological model was revised, and a three-dimensional groundwater flow and chloride transport model was developed using MODFLOW 6. The Llobregat Delta is a key water resource, but infrastructure development has increased vulnerability to saline intrusion. A MODFLOW 6 model simulated variable-density groundwater flow and chloride transport, ensuring accurate representation of tunnels, retaining walls, and geological formations. Three simulation scenarios were performed: comparing the aquifer’s present state with a scenario without infrastructure, introducing infrastructure elements at their construction dates to analyze cumulative changes, and modeling each element separately. Simulations show infrastructure significantly modifies groundwater flow. The inner dock had the greatest impact, promoting seawater ingress. Findings highlight the need for improved geological understanding, best construction practices, and strategic infrastructure placement to protect groundwater resources.