Rapid population growth and increasing food demand have impacts on the environment due to the generation of residues, which could be managed using sustainable solutions such as the circular economy strategy (waste generated during food processing must be kept within the food chain). Reusing discarded fish remains is part of this management strategy, since they contain high-value ingredients and bioactive compounds that can be used for the development of nutraceuticals and functional foods. Fish side streams such as the head, liver, or skin or the cephalothorax, carapace, and tail from shellfish are important sources of oils rich in omega-3. In order to resolve the disadvantages associated with conventional methods, novel extraction techniques are being optimized to improve the quality and the oxidative stability of these high-value oils. Positive effects on cardiovascular and vision health, diabetes, cancer, anti-inflammatory and neuroprotective properties, and immune system improvement are among their recognized properties. Their incorporation into different model systems could contribute to the development of functional foods, with market benefits for consumers. These products improve the nutritional needs of specific population groups in a scenario where noncommunicable diseases and pandemic crises are responsible for several deaths worldwide.