The rapid expansion of the aquaculture industry is accompanied by high organic and nutrient loadings from formulated feeds. This leads to water deterioration and pathogenic microorganisms. Natural biota (e.g., bacteria, phytoplankton, zooplankton, and zoobenthos) in ponds form important parts of cultured aquatic animals’ diets. They contain essential proteins, lipids, carbohydrates, amino acids, and fatty acids and are considered promising supplementary nutrition sources for cultured aquatic animals. Particularly, they are available to aquatic animals throughout the day, and an adequate supply of them as starter foods during the larvae stage ensures high survival. Since formulated feeds constitute more than 50% of aquaculture production costs, optimizing the utilization of natural biota and reducing dietary nutrient input without compromising animals’ growth should be a priority to improve the economic success and sustainability of aquaculture. From this scenario, the present review offers an updated view of the natural biota category in aquaculture systems, their nutritional components, and their contributions to the growth of cultured aquatic animals. Taken together, this review emphasizes the significant roles of natural biota playing in the growth of aquatic animals and encourages maximizing utilization of natural biota to improve feed conversion efficiency and aquaculture sustainability.