In the context of the COBO project (funded by EU FP 6), consequences of a fish farm activity on biogeochemistry composition and processes of bottom sediments below the fish farm cages have been evaluated. The fish farm was located in a northern fjord (Loch Creran, Scotland). The study was carried out three months after the removing of the cages. Seven cores in May and three cores in August 2006 were collected to study early diagenesis processes and to calculate benthic fluxes. Each core was extruded; pore waters were extracted and analyzed for nutrients (NH3, NO3, NO2, PO4, Si(OH)4, and TCO2), metals (Fe and Mn) and sulphates; diffusive fluxes at the sediment-water interface were calculated by applying Ficks first law. Preliminary results show sediments lying down to the fish farm were characterized by more intensive early diagenesis processes (from 2 to 4 times more than blank area). This means the fish farm produce high reactive organic matter snow that increases the reactivity of bottom sediments. Seasonal variations with increased diagenetic processes in summer were also recorded. In spring and in summer sediments both from the impacted area and the control sites were affected by strong bio-irrigation processes. Calculated benthic fluxes reflect the early diagenesis patterns with more intensive nutrient fluxes to the overlying water in the fish farm affected area and in the summer season, this suggests sediments affected by fish farm activity contribute more to eutrophication of confined coastal waters.