The aim of this paper is to outline the potential of imaging spectrometry and GIS techniques as tools for the monitoring of coastal sea waters and for the management of industrial/agricultural pollution phenomena. A specific flight was realized on September 30, 1999 using a hyperspectral MIVIS sensor that collected data in 102 spectral channels between 0.43 and 12.7 micrometers . Hyperspectral aerial images have been processed in order to obtain updated and accurate water quality maps. Furthermore important information on bathymetry, sea bottom features and hydrodynamic circulation have been derived from image processing and on-site surveys. The obtained information layers have been inserted in a specific GIS database and integrated with further information. The processing of data layers was performed, using a dedicated software, through typical GIS operators like indexing, recording, matrix analysis, proximity analysis. The interactions between sea water, industrial installations, agricultural areas, water resources, urban settlements and natural risks have been analyzed. This allowed the creation and processing of different thematic layers like quality, vulnerability, risk and impact maps.