Nitrogen fixation is a vital process in biogeochemical cycles within ecosystems. While current research on nitrogen fixation in aquatic ecosystems has mainly focused on marine environments, studies on waters, such as lakes, have only recently begun. To understand current research hotspots and development trends regarding nitrogen-fixing microorganisms in freshwater lakes, this study examined literature on the topic from the Web of Science database. CiteSpace and VOSviewer were used to construct and analyze knowledge maps, revealing current research hotspots and future research trends in this field. Based on these findings, we conducted a literature integration analysis to outline the effects of nitrogen and phosphorus nutrients on nitrogen fixation rates in water and their underlying mechanisms. The results show that: (1) From 1992 to 2024, the number of publications and citations in the field of nitrogen-fixing microorganisms in global freshwater lakes has steadily increased. (2) National, author and institutional collaboration network analyses indicate that research on nitrogen-fixing microorganisms in freshwater lakes is an interdisciplinary field involving cooperation among multiple countries and institutions. (3)Cluster analysis reveals that research hotspots mainly focus on: nutrient control strategies under phosphorus limitation and their impact on cyanobacterial community succession; the analysis of nitrogen-fixing microbial diversity based on thenifH gene; and the functional characterization of this gene in the nitrogen cycle. The analysis also reveals long-term dynamic changes in phytoplankton community composition driven by environmental factors. (4) The results of the integration analysis indicate that: the geographical distribution of nitrogen fixation quantification studies is imbalanced. North America has established a comprehensive indicator system covering various water types. In contrast, Asia and South America focus on describing cyanobacterial biomass, while Europe primarily focuses on the dynamic changes of nitrogen and phosphorus, as well as the coupling relationship of the nitrogen fixation process. Research on nitrogen-fixing species mainly centres on the phylum Cyanobacteria (e.g.,Nostoc andDolichospermum), while other phyla such as Proteobacteria and Archaea are relatively scarce. Total phosphorus shows a significant positive correlation with nitrogen fixation rates, whereas total dissolved nitrogen, nitrate nitrogen and ammonium nitrogen show significant negative correlations. Non-linear segmented model fitting revealed a critical value of 25μg/L for total phosphorus in regulating nitrogen fixation rates in freshwater lakes. Future research on nitrogen fixation processes urgently requires standardised measurement methods (e.g., acetylene reduction and isotope tracing) and metric units (e.g., area/volume) to improve the comparability of research results. This study summarises changes in the research hotspots and frontiers of nitrogen-fixing microorganisms in freshwater lakes over the past 30 years, suggesting that our understanding of nitrogen fixation processes and their ecological contributions should continue to expand by incorporating diverse analytical indicators (e.g., enzyme activity and transcriptomics), standardized analytical procedures and multi-indicator fusion evaluation methods.