Abstract The impacts of climate change and environmental management policies on the Mediterranean Sea were analyzed in multi-annual simulations of carbon cycling in a planktonic ecosystem model. The modeling system is based on a high-resolution coupled physical–biogeochemical ocean model that is off-line and forced by medium-resolution global climate simulations and by estimates of continental and river inputs of freshwater and nutrients. The simulations span the periods 1990–2000 and 2090–2100, assuming the IPCC SRES A1B scenario of climatic change at the end of the century. The effects of three different options on land use, mediated through rivers, are also considered. All scenarios indicate that the increase in temperature fuels an increase in metabolic rates. The gross primary production increases approximately 5% over the present-day figures, but the changes in productivity rates are compensated by augmented community respiration rates, so the net community production is stable with respect to present-day figures. The 21st century simulations are characterized by a reduction in the system biomass and by an enhanced accumulation of semi-labile dissolved organic matter. The largest changes in organic carbon production occur close to rivers, where the influence of changes in future nutrient is higher.