This study analyzed fatty acid profiles in liver, gonad, and fillet tissues of Moroccan silver carp (Hypophthalmichthys molitrix) and common carp (Cyprinus carpio) at mature and immature stages. Polyunsaturated fatty acids (PUFAs) were abundant in mature gonads and fillets of both species, with ω-3 fatty acids significantly higher in common carp gonads and ω-6 fatty acids significantly higher in silver carp gonads. The findings suggest that fish waste tissues (liver and gonads) are valuable sources of bioactive fatty acids and could be repurposed for nutraceutical, pharmaceutical, or aquaculture feed applications under circular economy principles.