The concentrations of six heavy metals (cadmium [Cd], chromium [Cr], copper [Cu], manganese [Mn], lead [Pb], and zinc [Zn]) were determined in liver and brain of nine species of waterfowl from the Evros Delta, one of the most important wetlands in Greece, to assess metal contamination and potential risk to waterfowl. Significant differences among species were found for hepatic Cr, Cu, Pb, and Zn; the highest levels of all metals were found in liver of mute swans. Cd increased significantly with age in both organs of wigeon; some differences were also observed between males and females of the same species. Feeding habits were found to significantly affect hepatic Cr, Zn, and Cu concentrations with greater concentrations found in herbivorous than omnivorous species. Several significant positive correlations between metals were detected mainly in liver samples, which were attributable either to their association to metallothioneins or to common routes of exposure of waterfowl. Hepatic and cerebral concentrations of Cd and Pb correlated positively. Given the discrepancies in the thresholds or critical levels of metals in tissues of waterfowl, our survey showed that environmental exposure to increased levels of heavy metals may threaten, at least to some degree, the populations of waterfowl wintering in the Evros Delta. In a small percentage of birds, values indicative of severe adverse effects were determined. Swans that had been found dead showed some of the highest values, whereas accumulation levels did not follow a consistent pattern among the ducks examined.