This study evaluated how estuary of origin and ontogenetic stage influence the fatty acid (FA) composition in the tissues of wild European sea bass juvenile. We evidenced tissue-specific patterns, with the brain exhibiting a distinct FA composition from the liver and muscle. Ontogenetic stage and estuary influenced the general FA profile, and particularly the essential FA (EFA) like docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA) in all tissues. The data also revealed the ability of wild sea bass to modulate, at the molecular level, FA biosynthesis pathways and suggest a potential dietary DHA limitation in the natural environment. The distribution of FA within tissues might reflect shifts in diet, metabolic demands, or adaptations to environmental conditions. This study provides insights about FA dynamics in euryhaline fish during juvenile life stage, improving our understanding of the metabolism need and EFA trophic availability in a changing environment.