Recirculating aquaculture systems (RAS) have emerged as a sustainable aquaculture technology because of their high water-use efficiency, enhanced biosecurity, and reduced environmental impact. However, disease outbreaks, microbial instability, and deterioration of water quality remain major constraints affecting fish health and productivity. Probiotics have been found to improve growth performance, feed utilization, host immune response, and disease resistance. However, the underlying mechanisms, research evolution, collaboration patterns, and emerging research hotspots related to probiotic integration in RAS are not yet fully understood. This study provides a comprehensive analysis by integrating bibliometric analysis with a systematic review to evaluate the mechanisms through which probiotics improve fish health and water quality in RAS. Based on the selected keywords (“probiotics” OR “microbial community” OR “gut microbiota”) AND (“recirculating aquaculture system” OR “RAS” OR “water recirculation system”) AND (“fish” OR “aquaculture”), a PRISMA-guided systematic search of the Scopus database identified 376 studies published from 2001-2025. Following the extraction of metadata, the Bibliometrix app of R software (v.4.5.2) and VOSviewer (v. 1.6.20) were used to analyze publication trends, country collaboration, co-authorship networks, and keyword co-occurrence. Results revealed a rapid increase in publications after 2007, with China emerging as the leading contributor and the keyword mapping identified water quality, microbial communities, gut microbiota, and disease resistance as the major research hotspots. Mechanistic evidence demonstrated that probiotics enhance fish health by modulating gut microbiota, improving immune response, suppressing pathogenic microorganisms, and promoting nutrient cycling and biofilter performance within RAS. The findings indicate that future research is required to optimize probiotic strain selection, dosage, long-term stability, and standardized application strategies for farmed fish species in RAS. Overall, this study provides a comprehensive understanding of probiotic-mediated mechanisms in RAS, identifies current research gaps, and outlines future research perspectives to facilitate the development of more sustainable and resilient RAS-based aquaculture systems.