Regular consumption of adequate quantities of lipids rich in omega-3 fatty acids is claimed to provide a broad spectrum of health benefits, such as inhibiting inflammation, cardiovascular diseases, diabetes, arthritis, and ulcerative colitis. Lipids isolated from many marine sources are a rich source of long-chain polyunsaturated fatty acids (PUFAs) in the omega-3 form which are claimed to have particularly high biological activities. Functional food products designed to enhance human health and wellbeing are increasingly being fortified with these omega-3 PUFAs because of their potential nutritional and health benefits. However, food fortification with PUFAs is challenging because of their low water-solubility, their tendency to rapidly oxidize, and their variable bioavailability. These challenges can be addressed using advanced encapsulation technologies, which typically involve incorporating the omega-3 oils into well-designed colloidal particles fabricated from food-grade ingredients, such as liposomes, emulsion droplets, nanostructured lipid carriers, or microgels. These omega-3-enriched colloidal dispersions can be used in a fluid form or they can be converted into a powdered form using spray-drying, which facilitates their handling and storage, as well as prolonging their shelf life. In this review, we provide an overview of marine-based omega-3 fatty acid sources, discuss their health benefits, highlight the challenges involved with their utilization in functional foods, and present the different encapsulation technologies that can be used to improve their performance.