Binhai New Area (BHNA), as one of the most economically and industrially regions in the Haihe River Basin, China, is seriously affected by seawater intrusion and groundwater over-exploitation. Groundwater vulnerability assessment (GVA) is an effective tool to protect the groundwater resources from being polluted. In this study, vertical and horizontal groundwater conditional factors were first assessed separately by two different models. The AHP-DRASTIC model was used to evaluate the intrinsic groundwater vulnerability and the AHP-GALDIT model was used to evaluate the specific groundwater vulnerability to seawater intrusion. Then, a GIS-based overlaying approach was used to get the comprehensive shallow groundwater vulnerability. The results of the comprehensive model showed that the vulnerability areas of very low, low, medium, and high account for 1.37%, 11.36%, 60.56%, and 26.71%, respectively. Finally, to effectively manage the groundwater in the study area, two remediation areas, two control areas, and one protected area were determined based on the comprehensive groundwater vulnerability maps. This study can not only promote the development of rational exploitation of shallow groundwater and prevention of groundwater pollution in BHNA but also provide a framework for future research in the GVA on the coast.