The recent growth of aquaculture has increased the risks associated with disease outbreaks, excessive use of antibiotics, antimicrobial resistance, and sustainable environmental management. Recent evidence has emphasized the potential of probiotics as novel biological resources for enhancing fish health and production efficiency. Probiotics, given as feed or water supplements, improve growth performance, feed efficiency, immune ability, and metabolism in aquatic animals. The fish gut contains a diverse and complex microbial community that is primarily involved in digestion, nutrient uptake, and immune responses. Probiotic supplementation can modulate this core microbiota, increase digestive enzyme secretion, and optimize lipid, carbohydrate, and protein metabolism, leading to improved feed conversion efficiency and physiological resistance. Moreover, probiotics can boost innate immunity by competitive exclusion, production of antimicrobial substances, and regulation of immune-related gene expression. Current developments focus on host-specific strain selection and the development of next-generation probiotics. In this way, probiotics play a significant role in sustainable aquaculture, as they reduce the use of antibiotics and minimize waste output in the environment. In conclusion, probiotics are essential elements in precision health management approaches. They promote productivity, disease resistance, and sustainability in modern aquaculture.