Remote imaging spectroscopy from 400 to 800 nm can use benthic reflectance signatures to map the composition and condition of shallow water ecosystems. We present a novel probabilistic approach to jointly estimate the seafloor reflectance and water properties while flexibly incorporating varied domain knowledge and in situ measurements. The inversion transforms remote radiance data with an atmospheric correction followed by a water column correction. Benthic reflectance and water optical properties are both represented by linear mixtures of endmember spectra. We combine remote measurements, prior knowledge and field data using a flexible Bayesian optimal estimation, solving for the Maximum A Posteriori (MAP) combination of water column properties, seafloor reflectance, and depth. We then demonstrate performance in controlled simulations and in overflights of a coral reef in Hawaii with coincident in situ measurements. The measurement approach helps lay a foundation for wide-area airborne mapping of the condition of threatened coastal ecosystems such as coral reefs.
