Aquatic organisms play a pivotal role in safeguarding global ecological security and biodiversity. In order to reveal the evolution law, research hotspots and cooperation pattern of global wetland aquatic biodiversity research, this study employs bibliometric methods to analyze published literature retrieved from the Web of Science Core Collection. The search terms “aquatic biodiversity” and “wetland” were used for a topic-based search covering the period from 2003 to 2022. Analytical tools including Excel, VOSviewer, and Scimago Graphica were utilized to conduct a comprehensive bibliometric analysis of wetland aquatic biodiversity research from multiple dimensions of publishing trend, country, institution, highly cited literature, keyword clustering and international cooperation. The results revealed a gradual upward trend in wetland aquatic biodiversity research from 2003 to 2022. Beyond fundamental investigations into wetland ecosystems and aquatic organisms, research attention had increasingly focused on ecosystem restoration and ecosystem services resulting from changes in wetland ecosystems. The United States, Brazil, and Australia emerged as the leading countries in this research domain. The French National Centre for Scientific Research had published the highest number of papers and maintained exceptionally close collaborative relationships with other institutions. The most frequent international collaboration occurred between China and the United States, both of which played crucial roles in fostering partnerships with other nations. Global research hotspots in wetland aquatic biodiversity could be primarily categorized into four clusters: aquatic ecosystem development, aquatic biological community structure, impacts on aquatic biodiversity, and ecological problems induced by human activities. Currently, wetland aquatic biodiversity research is in a developmental phase with stable growth potential. While China has achieved a leading position in terms of publication output internationally, challenges remain including imbalanced research layout, insufficient cross-disciplinary integration, and weak exploration of core scientific mechanisms. Future efforts should focus on establishing standardized long-term monitoring networks and deepening multi-dimensional mechanistic research to provide scientific support for wetland aquatic biodiversity conservation and sustainable development.