Temporal variation in the extent of submerged macrophytes along the littoral zone of Sirmione Peninsula in the southern part of Lake Garda (Northern Italy) was investigated using imaging spectrometry. Two images, with a spatial resolution of 5 m were acquired by the Multispectral Infrared and Visible Imaging Spectrometer (MIVIS) in the summers of 1997 and 2005. Image data were first geocoded and then corrected for both atmospheric and skylight reflection effects at the water surface using the 6S radiative transfer code. The two images were inverted using a bio-optical model, which was parameterised with the inherent optical properties of the lake. The inversion utilized the spectral range from 0.48-0.60 μm because it simultaneously provided the lowest environmental noise and the best atmospheric correction performances for the two scenes and produced images of bottom depth and of two substrate classes: bare sand and submerged vegetation, representing a mixture of valuable freshwater species. The MIVIS-derived bottom depth ranges and patterns were comparable to a bathymetry chart with a deviation less than 5%. In 2005, the image was consistent with contemporaneous in-situ derived knowledge on macrophyte distribution. In 1997, the substrate image map was deemed reasonable with respect to the macrophyte distribution documented in 2000. The comparison of the substrate products for the two dates showed a marked decrease in macrophyte beds, with a concomitant increase in sandy substrates. In the 8-year interval the extent of submerged macrophyte decreased from 72% to 52%. We expect that this study will contribute to increased knowledge of macrophyte colonisation patterns of the Sirmione Peninsula, where, despite their ecological significance, changes have been poorly documented.