Cover crops provide ecosystem services such as storing atmospheric carbon in soils after incorporation of their residues. Cover crops also influence soil water balance, which can be an issue in temperate climates with dry summers as for example in southern France and Europe. As a consequence, it is necessary to understand cover crops’ long-term influence on greenhouse gases (GHG) and water balances to assess their potential to mitigate climate change in arable cropping systems. We used the previously calibrated and validated soil-crop model STICS to simulate scenarios of cover crop introduction to assess their influence on rainfed and irrigated cropping systems and crop rotations distributed among five contrasted sites in southern France from 2007-2052. Our results showed that cover crops can improve mean direct GHG balance by 315 kg CO2e ha-1 yr-1 in the long term compared to that of bare soil. This was due mainly to an increase in carbon storage in the soil despite a slight increase in N2O emissions which can be compensate by adapting fertilization. Cover crops also influence the water balance by reducing mean annual drainage by 20 mm yr-1 but increasing mean annual evapotranspiration by 20 mm yr-1 compared to those of bare soil. Using cover crops to improve the GHG balance may help to mitigate climate change by decreasing CO2e emitted in cropping systems which can represent a decrease from 4.5 to 9% of annual GHG emissions of the French agriculture and forestry sector. However, if not well managed, they also could create water management issues in watersheds with shallow groundwater. Relationships between cover crop biomass and its influence on several variables such as drainage, carbon sequestration and GHG emissions could be used to extend our results to other conditions to assess the cover crops influence in a wider range of areas.