Estuaries are generally considered as key habitats for early life stages of fish. However, in the face of massive destruction of many estuarine intertidal areas, management and conservation measures are needed. Fish condition indicators may be used as proxy of habitat quality, which may provide valuable information for management of coastal areas. In this study, post-larvae of golden mullet (Chelon auratus) and European glass eels (Anguilla anguilla) were sampled in three sites in the Gironde estuary. Different lipid classes and fatty acids were quantified: phospholipids (globally, phosphatidylethanolamine and phosphatidylcholine), triglycerides, omega-3 (particularly docosahexaenoic and eicosapentaenoic acids), omega-6 and 18:1. These biomarkers provide information on the nutritional status of the larvae as well as on prey availability between sites. One site (the middle site, called SII) significantly differed from the others as it seemed to offer abundant and better quality prey. The very high levels of omega-3 contained in the post-larvae suggested that they fed preferentially on diatoms. However, the post-larvae of golden mullet that colonised this site also showed physiological stress that could be explained by exposure to pollutants through their prey.