Northern inland waters emit CO2 and CH4 to the atmosphere but the importance of these emissions is poorly understood due to a lack of integrated catchment-scale estimates of carbon (C) emissions from lakes and streams. In this study we quantified the annual emission of CO2 and CH4 from 27 lakes and 23 stream segments in a 15 km2 subarctic catchment in northern Sweden. All lakes and streams were net sources of C to the atmosphere on an annual basis. Streams dominated (96%) the aquatic CO2 emission while lakes (61%) dominated the aquatic CH4 emission. Total aquatic C emission from the catchment was estimated to be 9.1 g C m−2 yr−1 (98% as CO2). Although streams only accounted for 4% of the aquatic area in the catchment, they accounted for 95% of the total emission. The C emissions from lakes and streams were considerably larger than previously reported downstream waterborne export of C from the catchment, indicating that the atmospheric losses of C in the aquatic systems are an important component in the catchment C balance.