The potential of Hyperion images acquired on September 2001 (receding flood period of the Amazon River) and June 2005 (high flood) was investigated for reflectance characterization of selected Amazon floodplain waterbodies using a linear spectral mixture model. The results show the ability of Hyperion to measure adequately the major variation in water reflectance spectral features in response to the annual flood pulse of the Amazon River. Mixture model fraction values were correlated with measured inorganic suspended solids (ISS) but not with chlorophyll (Chl) in the high flood period. Inspection of the fractions across the two images revealed variation in water composition. Small changes in ISS- and Chl-bearing water fractions between the images indicated relatively stable spectral conditions for low (Tapajos River and Lake Juruparipucu) and high (Amazon River) turbidity waterbodies. Large changes indicated reflectance variation in some lakes when the water receded due to algal blooms (Lake Curumu) and sediment resuspension in shallow regions (Lake Aritapera). Although not all water constituents were modelled adequately for quantification purposes, spectral mixture modelling is still an interesting approach for spectral-temporal reflectance characterization of Amazonian floodplains with hyperspectral data.