Based on a 2-year monitoring study, we found that the freshwater system of the Danube Delta, Romania, releases carbon dioxide and methane to the atmosphere. The amount of carbon released depends on the freshwater feature (river branches, channels and lakes), season and hydrologic condition, affecting the exchange with the wetland. Spatial upscaling should therefore consider these factors. Furthermore, the Danube Delta increases the amount of carbon reaching the Black Sea via the Danube River.