Abstract: Seawater intrusion is a global environmental geological issue that poses a serious threat to the water supply security and ecological environment of coastal cities. Microorganisms exhibit a high sensitivity to environmental changes, and in recent years, numerous scholars have turned their attention to the response characteristics of microorganisms to seawater intrusion, offering new perspectives and methodologies for research in this field. To completely understand the research progress in this field, this study, based on the Web of Science core database, employed bibliometric visualization analysis methods to analyze the current status, hotspots, and trends of research on microbial response characteristics to seawater intrusion. The results indicate that significant developments in this emerging research area have mainly occurred after 2011, with a consistent increase in publication volume and citation counts. Chinese scholars actively engage in the research of microbial responses to seawater intrusion, ranking second in terms of both publication output and h-index, with a significant academic impact. Keyword cluster analysis reveals that popular research topics in this field encompass the response of groundwater microbial communities to seawater intrusion, investigations into soil microbial communities’ response to seawater intrusion, and the geochemical cycling of elements in conjunction with microbial processes. The study indicates that the succession of microbial communities in brackish-saline water transition zones is jointly influenced by factors such as salinity, dissolved oxygen, temperature, organic carbon, and pH. The primary controlling factors vary with hydrogeological conditions. The intrusion of seawater impacts microbial-mediated processes involved in the cycling of carbon, nitrogen, sulfur, iron, and other substances. The identification of typical marine bacteria and halophilic archaea found in aquifers holds significant indicative value concerning seawater intrusion. This serves as a potent complement to traditional investigative methods for seawater intrusion, offering substantial potential and advantages in distinguishing paleoseawater intrusion and seawater intrusion.