The spectral reflectance of 3 species of seagrass was measured in different habitats at 3 estuaries in southeastern Australia during each of the 4 seasons of 2000. Seagrass species were spectrally distinct regardless of whether the leaves were fouled by epibionts even though spatial and temporal variability in reflectance was observed within each species. The visible wavelengths that penetrate water fortunately coincide with the regions of maximum absorption by plant photosynthetic and accessory pigments. Mapping of benthic plants to species level is possible using a hyperspectral sensor that has narrow bands centred on pigment-related spectral features in the visible, e.g. the programmable wavebands of the CASI (Compact Airborne Spectrographic Imager).