In the context of the EU funded COBO project, consequences of fish farm activities on bio-geochemical processes in surface sediments of a Northern fjord (Loch Creran, Scotland) has been studied. Seven cores in May and three cores in August 2006 were collected to study early diagenesis processes and benthic fluxes. Each core was extruded, pore waters were extracted and analyzed for nutrients (NH3, NO3, NO2, PO4, Si(OH)4, TCO2), metals (Fe, Mn) and sulphates; diffusive fluxes at the sediment-water interface were calculated. Preliminary results show that the area, affected by fish farm wastes, is characterized by more intensive early diagenesis benthic processes (from 2 to 4 times more than unaffected area) due to higher reactive organic matter inputs to the sediment. Seasonal variations with increased diagenetic processes in summer were also recorded. In spring and in summer both, sediments from the impacted area and the control site are 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.