Understanding the drivers of climate change requires knowledge about the global carbon (C) cycle. Although inland waters play an important role in the C cycle by emitting and burying C, streams and lakes are in general overlooked in bottom-up approached C budgets. In this thesis I estimated emissions of carbon dioxide (CO2) and methane (CH4) from all lakes and streams in a 15 km2 subarctic catchment in northern Sweden, and put it in relation to the total catchment C exchange. I show that high-latitude aquatic systems in general and streams in particular are hotspots for C emission to the atmosphere. Annually, the aquatic systems surveyed in this study emitted about 10.8 ± 4.9 g C m-2 yr-1 (ca. 98 % as CO2) which is more than double the amount of the C laterally exported from the catchment. Although the streams only covered about 4% of the total aquatic area they emitted ca. 95% of the total aquatic C emission. For lake emissions, the ice break-ups were the most important annual events, counting for ca. 45% of the emissions. Overall, streams dominated the aquatic CO2 emission in the catchment while lakes dominated CH4 emission, 96 % and 62 % of the totals, respectively. When summing terrestrial and aquatic C fluxes together it showed that the aquatic emissions alone account for approximately two thirds of the total annual catchment C loss. The consequence of not including inland waters in bottom-up derived C budgets is therefore a risk of overestimating the sink capacity of the subarctic landscape. However, aquatic systems can also act as C sinks, by accumulating C in sediment and thereby storing C over geological time frames. Sediment C burial rates were estimated in six lakes from a chronology based on 210Pb dating of multiple sediment cores. The burial rate ranged between 5 - 25 g C m-2 yr-1, which is of the same magnitude as lake C emissions. I show that the emission:burial ratio is about ten times higher in boreal compared to in subarctic-arctic lakes. These results indicate that the balance between lakes C emission and burial is both directly and indirectly dependent on climate. This process will likely result in a future increase of C emissions from high-latitude lakes, while the C burial capacity of these same lakes sediments weaken.