Coastal nursery areas are subjected to a wide range of natural and anthropogenic stressors, including global warming, which indirectly influence trophic food webs. A global rarefaction of n-3 polyunsaturated fatty acids (PUFA) in trophic networks is in progress. The aim of this study was to assess the effect of a reduction in the dietary availability of n-3 PUFA on some molecular and biochemical parameters related to lipid metabolism and oxidative stress response in juvenile European sea bass (Dicentrarchus labrax) raised at two temperatures (15 °C and 20 °C). Fish were fed for five months with a reference diet (RD; 1.65% n-3 PUFA on a dry matter basis, DM), used as a proxy of trophic networks where n-3 PUFA is plentiful, and a lower n-3 PUFA diet (LD; 0.73% n-3 PUFA DM), designed to mimic a decrease in n-3 PUFA resulting from global changes (the n-3 PUFA levels tested remained above the nutritional minimum required for this species). Results showed that diet did not affect the hepatic expression of some mRNA coding for transcriptional factors involved in regulating the metabolic pathways related to fatty acid bioconversion. Although our molecular analysis was limited to transcript expression, these data suggest the presence of a threshold in the nutritional supply of PUFA above which the activation of these molecular pathways does not occur. However, the expression for most of the transcripts tested was up-regulated at 20 °C. Despite the high peroxidation index in fish fed RD, very few modifications of the oxidative stress response were associated with diet. At 20 °C, an increase of the enzymatic antioxidant response was observed, but there was no correlation with the peroxidation index or malondialdehyde products.