The aquaculture industry is under the framework of the food-water-energy nexus due to the extensive use of water and energy. Sustainable practices are required to support the tremendous growth of this sector. Currently, the aquaculture industry is challenged by reliance on capture fisheries for feed, increased use of pharmaceuticals, infectious outbreaks, and solid/liquid waste management. This review posits microalgal technology as a comprehensive solution for the current predicaments in aquaculture in a sustainable way. Microalgae are microscopic, freshwater and marine photosynthetic organisms, capable of carbon mitigation and bioremediation. They are indispensable in aquaculture due to their key role in marine productivity and their position in the marine food chain. Microalgae are nutritious and are currently used as feed in specific sectors of aquaculture. Due to their bioremediation potential, direct application of microalgae in shellfish ponds and in recirculating systems have been adopted to improve water quality and aquatic animal health. The potential of microalgae for integration into various aspects of aquaculture processes, namely hatcheries, feed, and waste management has been critically analyzed. Seamless integration of microalgal technology in aquaculture is feasible, and this review will provide new insights into using microalgal technology for sustainable aquaculture.