Abstract Carbon storage, processing, and transport in freshwater systems are important components of the global carbon cycle and sensitive to global change. However, in large-scale modeling this part of the boundless carbon cycle is often lacking or represented in a very simplified way. A new process-oriented lake biogeochemical model is used for investigating impacts of changes in atmospheric CO2 concentrations and organic carbon loading from the catchment on future greenhouse gas emissions from lakes across two boreal to subarctic regions (Northern Sweden and Alaska). Aquatic processes represented include carbon, oxygen, phytoplankton, and nutrient dynamics leading to CO2 and CH4 exchanges with the atmosphere. The model is running inside a macroscale hydrological model and may be easily implemented into a land surface scheme. Model evaluation demonstrates the validity in terms of average concentration of nutrients, algal biomass, and organic and inorganic carbon. Cumulative annual emissions of CH4 and CO2, as well as pathways of CH4 emissions, also compare well to observations. Model calculations imply that lake emissions of CH4 may increase by up to 45% under the Representative Concentration Pathway 8.5 scenario until 2100, and CO2 emissions may increase by up to 80% in Alaska. Increasing organic carbon loading to the lakes resulted in a linear response in CO2 and CH4 emissions across both regions, but increases in CO2 emissions from subarctic lakes in Sweden were lower than for southern boreal lakes, probably due to the higher importance of imported vegetation-?generated? inorganic carbon for CO2 emission from subarctic lakes.