Climate change induced mass loss of the Greenland Ice Sheet increases the amount of meltwater, which is mainly released into the numerous fjords along the coast of Greenland. Due to its low salinity and high silt load, meltwater can profoundly affect the biogeochemical cycling of carbon. We visited the world’s largest fjord system, Scoresby Sund at the eastern coast of Greenland, and its northernmost branch, Nordvestfjord, in the summer of 2016 for investigating biogeochemical carbon cycling. The data reveal that meltwater limited the productivity by inhibiting the resupply of nutrients to the surface and by shadowing the upper part of the water column by the introduction of silts. These silts, though, increased the export of organic carbon to depth by ballasting the sinking organic particles. While the region close to the fjord entrance was influenced by shelf waters, the water column within Nordvestfjord was significantly modulated by meltwater input from a number of marine- and land-terminating glaciers. Our results show that there was a clear gradient from a productive system with efficient remineralization at the mouth of the fjord to a less productive system with a high carbon export towards the inner fjord parts. These results imply that Scoresby Sund can be seen as a hotspot of carbon burial.