Freshwater lakes are an important component of the global carbon cycle through both organic carbon (OC) sequestration and carbon dioxide (CO2) emission. Most lakes have a net annual loss of CO2 to the atmosphere and substantial current evidence suggests thatbiologic mineralization of allochthonous OC maintains this flux. Because net CO2 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 hydrologic characteristics and net CO2 emission. We calculated NEP for calendar year 2004 using whole‐lake OC and inorganic carbon (IC) budgets, NEPOC and NEPIC, respectively, and compared the resulting values to measured annual CO2 flux from the lakes. In both lakes, NEPOC and NEPIC were positive, indicating net autotrophy. Therefore CO2 emission from these lakes was apparently not supported by mineralization of allochthonous organic material. In both lakes, hydrologic CO2 inputs, as well as CO2 evolved from net calcite precipitation, could account for the net CO2 emission. NEP calculated from diel CO2 measurements was also affected by hydrologic 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 hydrologic sources of CO2 need to be accounted for when using CO2 concentrations to infer lake NEP.