Heavy metals and organic pollutants were investigated in the Adour estuary (South West France) and associated wetlands using the European eel (Anguilla anguilla) as a bioindicator. Heavy metals (Cu, Cd, Zn, Pb, and Ag) were measured in soft tissue of yellow eels. Mercury (total Hg and MeHg) and organochlorinated compounds (7 PCBs, 11 OCPs) were analysed in muscle. Concentrations in muscle were in agreement with moderately contaminated environments in Europe and were below the norms fixed for eel consumption for heavy metals and OCPs. Analyses of liver showed a higher pressure of Ag and Zn in the downstream estuary than in the freshwater sites whereas Cd was lower in the estuary probably because of the salinity influence. According to quality classes 100% of eels from freshwater sites indicated clean or slightly polluted environments. However, total mercury concentrations were close to the thresholds fixed by the European Community in the downstream estuary, whereas the sum of PCBs was found to be greatly above the fixed value. 100% of the individuals from the estuary were classified in quality classes corresponding to polluted or highly polluted sites. These first results highlight the need of further investigations focused on mercury and PCBs in this area taking the seasonal temperature influence into account for a better understanding of the pollution distribution and the possible threat on the eel population from the Adour basin.