This study examines the uncertainty associated with two commonly used GIS-based groundwater vulnerability models, DRASTIC and EPIK, in assessing seawater intrusion, a growing threat along coastal urban areas due to overexploitation of groundwater resources. For this purpose, concentrations of Total Dissolved Solids (TDS) in groundwater samples at three pilot areas along the Eastern Mediterranean were compared with mapped vulnerability predictions obtained through DRASTIC and EPIK. While field measurements demonstrated high levels of groundwater salinity depending on the density of urbanization, both vulnerability assessment methods exhibited a limited ability in capturing saltwater intrusion dynamics. In the three pilot areas, DRASTIC was only able to predict correctly between 8.3 and 55.6% of the salinity-based water quality ranges, while EPIK's predictions ranged between 11.7 and 77.8%. This emphasizing that conventional vulnerability models perform poorly when anthropogenic impacts induce lateral flow processes such as seawater intrusion caused primarily by vertical groundwater extraction.