This study uses derivative spectroscopy to assess qualitative and quantitative information regarding seafloor types that can be extracted from hyperspectral remote sensing reflectance signals. Carbonate sediments with variable concentrations of microbial pigments were used as a model system. Reflectance signals measured directly over sediment bottoms were compared with remotely sensed data from the same sites collected using an airborne sensor. Absorption features associated with accessory pigments in the sediments were lost to the water column. However major sediment pigments, chlorophyll a and fucoxanthin, were identified in the remote sensing spectra and showed quantitative correlation with sediment pigment concentrations. Derivative spectra were also used to create a simple bathymetric algorithm.