The objective of this study was to evaluate fractions of metals (labile and pseudo-total) extracted from sediment samples collected in Itaipu Lake (boundary between Brazil and Paraguay) and to assess the dynamics and mobility of these fractions by identifying the same bioavailability and ecological risk to metals in the aquatic environment. The concentrations of metal ions were determined by flame atomic absorption spectrometry. There was a correlation between the metal ions, both in the labile and the pseudo-total, with regard to particle size. To assess metals concentrations in sediment, numerical sediment-quality guidelines were applied. The concentrations of aluminum, cadmium, iron, manganese, lead, and zinc in all sediment samples are lower than the proposed probable effects level (PEL), thus possibly indicating that there are no harmful effects from these metals. In contrast, concentrations of copper, chromium, and nickel exceeded the PEL in some samples, thus indicating that these stations are at potential risk. The level of contamination in sediments of Itaipu Lake for all metals was evaluated using contamination factor, degree of contamination, and sum-of-metals toxic unit.