The gut microbiome has a significant impact on fish nutrition, health, and their overall growth performance. This complex microbial community, which mostly lives in the gastrointestinal tract, has a dynamic interaction with its host, impacting digestion, nutrient absorption, immune responses, and disease resistance. The fish gut microbiota is extremely diverse and influenced by many factors, such as diet, environment, species, and aquaculture practices. Gut microbiota plays an important role in improving digestive functioning by producing enzymes that help in the breakdown of complex carbohydrates, proteins, and lipids, thereby improving the utilization of conventional and nonconventional feed ingredients. Additionally, it produces healthy components that are essential for fish growth and development, including amino acids, short-chain fatty acids, and vitamins. The microbiota improves immune defense by competing with harmful microbes, producing antimicrobial compounds, and modulating host immune responses. Dietary approaches, such as the use of probiotics, prebiotics, and synbiotics, have shown promise in improving fish health and performance by altering the composition of the gut microbiota. Furthermore, the use of microbial enzymes such as phytase in fish diets improves the bioavailability of nutrients such as phosphorus, reducing feed costs and environmental implications. Despite these developments, completely understanding of the intricate host-microbe interactions, as well as the effects of various dietary and environmental factors on gut microbial dynamics, remains a problem. The advent of next-generation sequencing and multi-omics technologies provides a unique opportunity to understand these intimate connections and develop sustainable solutions for improving fish nutrition and health. This chapter discusses the multifaceted roles of fish gut microbiota, with an emphasis on their importance in sustainable aquaculture practices. It implies recent scientific advances and future directions for improving nutrient utilization, reducing aquaculture waste, and strengthening fish welfare.