Groundwater pollution in the north coast of Mombasa is not only from surface sources but also from the intrusion of seawater via the Indian Ocean and creeks. This study assessed the vulnerability of the coastal aquifer to seawater intrusion using GALDIT index overlay method with the aid of GIS. Thematic maps of six major factors affecting seawater intrusion were prepared, and given appropriate weightages and ratings. These maps were overlaid, spatially analyzed to produce vulnerability maps and described based on low, moderate or high vulnerabilities. The results revealed a significant increase in percentage land cover for low vulnerability areas and a slight increase for high vulnerability regions between the pre-rains and the peak of raining season. The outcomes of this study provide useful insights on effective groundwater management for the study area.