The study focuses on the use of hyperspectral push-broom CASI2 and multispectral scanning ATM data to measure Colour Dissolved Organic Matter (CDOM), chlorophyll (Chl) and Suspended Particulate Matter (SPM) in complex optical Case 1 waters of the Straits of Messina and the Case 2 waters of the Venice Lagoon. In addition it is the aim to estimate macrophyte distribution during spring in the Venice Lagoon. The novel components of this work involve: . The integration of atmospheric and hydro-optical radiative transfer models (MODTRAN4 and Hydrolight 4.2) to estimate the underwater light field using matrix inversion techniques to derive CDOM, SPM and Chl. .Investigation to the potential to correct sun-glint on ATM/CASI data using ERS derived wind/wave data. . An investigation of the reflectance of submerged vegetation of a quasi-tidal shallow water lagoon.