The aim of this research is to investigate the capability of hyperspectral data in the identification of seagrass distribution and biomass compared to the present system of boat-mounted sonar systems. The current approach is very expensive and time-consuming and produces only sparse coverage of seagrass distributions. The first objective of this project is to obtain measurements of the nature and intensity of upwelling and downwelling radiation at different depths in the water column under a range of different water quality conditions. These measurements will be correlated with contemporaneous measurements of downwelling and upwelling radiation at the sea surface and at the aircraft sensor. The underwater spectral measurements will be used to develop and validate underwater radiative transfer models e.g. Hydrolight (Mobley, 1994) under a number of different illumination and observation configurations and over a range of representative homogeneous and heterogeneous substrate types. In support of the CASI acquisition surface and underwater spectroscopy measurements (Wettle et al, 2003) and a range of water quality measuring instruments will be deployed coincident with the CASI data acquisition. A coastal area of Crete selected as one of the Greek NATURA areas under the EC habitats directive has been identified as an excellent test site.