Robert G. Striegl G. R. Aiken D.O. Rosenberry T. C. Winter E.G. Stets 2009 Freshwater lakes are an important component of the global carbon cycle through both organic carbon (OC) sequestration and carbon dioxide (CO ₂) emission. Most lakes have a net annual loss of CO₂ to the atmosphere and substantial current evidence suggests that biologic mineralization of allochthonous OC maintains this flux. Because net CO ₂ flux to the atmosphere implies net mineralization of OC within the lake ecosystem, it is also commonly assumed that net annual CO₂ emission indicates negative net ecosystem production (NEP). We explored the relationship between atmospheric CO₂ emission and NEP in two lakes known to have contrasting hydrologie characteristics and net CO₂ emission. We calculated NEP for calendar year 2004 using whole-lake OC and inorganic carbon (IC) budgets, NEP_oc and NEP_IC, respectively, and compared the resulting values to measured annual CO ₂ flux from the lakes. In both lakes, NEP_Ic and NEP _Ic were positive, indicating net autotrophy. Therefore CO₂ emission from these lakes was apparently not supported by mineralization of allochthonous organic material. In both lakes, hydrologie CO₂ inputs, as well as CO₂ evolved from netcalcite precipitation, could account for the net CO₂ emission. NEP calculated from diel CO₂ measurements was also affected by hydrologie inputs of CO₂. These results indicate that CO₂ emission and positive NEP may coincide in lakes, especially in carbonate terrain, and that all potential geologic, biogeochemical, and hydrologie sources of CO₂ need to be accounted for when using CO₂ concentrations to infer lake NEP. Copyright 2009 by the American Geophysical Union. application/pdf 10.1029/2008JG000783 en Hydrologic support of carbon dioxide flux revealed by whole-lake carbon budgets article