Digestion, food absorption, immunological regulation, and disease resistance are all significantly influenced by the gut microbiota of freshwater aquaculture species. Recent developments in metagenomics, specifically next generation sequencing (NGS) and shotgun sequencing, have allowed scientists to go beyond straightforward microbe identification and do thorough functional assessment of fish gut ecosystems. Proteobacteria, Firmicutes, and Fusobacteriota are regularly found to be dominant in studies including tilapia, carp, and native freshwater species. Additionally, host genetics, nutrition, habitat, and environmental stressors have a significant impact on microbial structure and metabolic capability. Gaining an understanding of these microbial populations presents significant opportunity to enhance conservation, disease control, feed efficiency, and sustainable aquaculture development.