Background: Aquaculture supplies over half of global fish consumption but faces challenges including disease outbreaks, oxidative stress, antimicrobial resistance, and reliance on finite fishmeal and fish oil resources. Methods: This review synthesizes research on freshwater and marine microalgae, focusing on their bioactive compounds and functional roles in aquaculture nutrition and health. Results: Microalgae provide proteins, carotenoids, vitamins, polyunsaturated fatty acids, and immunostimulants that act via immunomodulation, antioxidant defense, gut microbiota regulation, anti-inflammatory activity, growth promotion, and pigmentation enhancement. Applications include live feed in larval rearing, dried biomass in compound feeds, and microalgal oils as fish oil substitutes. Conclusions: Incorporating microalgal nutraceuticals into aquafeeds offers a sustainable strategy to improve aquaculture productivity, animal health, and product quality, supporting the transition toward resilient and ecologically sustainable systems within the One Health framework.