Aquatic microbes, including algae, bacteria, and fungi found in both marine and freshwater ecosystems, are emerging as a novel and sustainable supply of bioactive compounds for food fortification. These microorganisms are rich in essential nutrients, such as vitamins, minerals, polyunsaturated fatty acids, proteins, and antioxidants, which are crucial for human health. Due to their ability to synthesize unique bioactive molecules, aquatic microbes offer a promising alternative to conventional sources for fortifying foods and enhancing their nutritional profile. Furthermore, their rapid growth and adaptability to diverse aquatic environments make them an attractive, scalable option for sustainable production. Incorporating these microbial-derived compounds into food products could address nutritional deficiencies, particularly in populations at risk of malnutrition, while promoting overall health and wellness. This book chapter highlights the potential of aquatic microbes as a sustainable and functional source for food fortification, focusing on their nutritional content, bioactive properties, and the technologies enabling their use in food systems. By integrating aquatic microbes into food fortification strategies, we can enhance the nutritional value of common food items, contributing to healthier diets and improving public health globally.