Interdisciplinary research indicated most critical ecological problems of semi-enclosed northern Adriatic ecosystem. We quantified mucilage-associated organic matter, characterised its chemical and biological composition and contributed to the knowledge of the mechanisms which lead to the massive accumulation of mucilage . A new device (TLS - double laser thermal lens spectrometer) was constructed. TLS-HPLC system was used for the determination of carotenoids and chlorophylls. The recently discovered parallel xanthophyll cycle in diatoms was confirmed. The system was used for the on-line monitoring of the cell lysis induced by addition of poly-APS. The trophic status of coastal waters impacted by municipal waste waters and fish farms was assessed using standard indices and a new complementary index based on relationships among chemotaxonomic phytoplankton pigments.The effectiveness of the artificial structures deployed in the water column near fish farms in reducing the impacts of mariculture was studied. Communities of fouling biota were assessed for uptake of particulate and dissolved matter. Biogeochemistry of mercury, in particular processes controlling methylation and demethylation, was studied in the estuarine and coastal waters. These processes proceed most actively in the surficial sedimentary layer and the MeHg produced is diffusing in the water column entering the food web. Biodiversity studies concentrated on coastal ichthyofauna as related to climatic and oceanographic changes. Genetic structuring of Pagellus erythrinus and Eledone moscata was studied isolating and sequencing microsatellites, population units of these two species in the Adriatic were estimated. A modified POM (Princeton Ocean Model) has been employed for simulation of circulation in the northern Adriatic and we developed a prognostic model of tides in the Adriatic sea which will be nested in the prognostic model of the Adriatic circulation.