Estuarine ecosystems hold significant importance within global ecosystems, and modeling serves as a crucial tool for analyzing them. With the continuous progress in this field, systematically reviewing the research on estuarine ecosystem modeling has become increasingly necessary, providing essential support for future advancements in this domain. This study employs bibliometric methods to analyze the relevant literature on estuarine ecosystem modeling from the Web of Science database, evaluating development trends, research status, hotspots, and regional characteristics. The results reveal that, since 1978, the number of publications related to estuarine ecosystem modeling has shown a general upward trend, attracting widespread attention from research institutions worldwide, with the United States leading in this field. The analysis of high-frequency keywords indicates that many scholars have conducted in-depth studies on estuarine ecosystems using modeling approaches, with “eutrophication” being a research hotspot. Cluster analysis results demonstrate that research on estuarine ecosystem modeling primarily focuses on three areas: environmental management, biogeochemical cycling, and food web dynamics. Comparing studies across different regions highlights significant regional disparities in this field. Compared to North America, Europe, and East Asia, estuarine ecosystem research in Africa, South America, and South Asia is relatively limited. Despite the unique ecological functions of estuarine ecosystems in these regions, they remain underexplored and understudied.