Greenland fjords receive considerable amounts of meltwater discharge from the Greenland Ice Sheet, influencing the physical and biogeochemical conditions within the fjords. Because ice melt will increase with ongoing climate change, research on present-day conditions is urgently needed to make better projections for the future. In the present study, a comprehensive analysis of the carbon cycle in Scoresby Sund, the world’s largest fjord system situated at the southeastern coast of Greenland, was conducted. In summer 2016, Scoresby Sund and its northernmost branch, Nordvestfjord, were visited. While the narrow Nordvestfjord is influenced by numerous marine-terminating glaciers and surface meltwater discharge, the wide Outer Scoresby Sund is much less affected by meltwater. Surface partial pressure of CO2, primary production, particulate organic carbon (POC) flux, and remineralisation within the water column are reported. The data reveal that meltwater significantly influenced the carbon dynamics within the fjord. First, meltwater itself increased the uptake of carbon dioxide from the atmosphere. Second, meltwater limited net community production in Nordvestfjord to 31 - 35 mmol C m-2 d-1 compared to the Outer Scoresby Sund and the shelf (43 - 67 mmol C m-2 d-1) by inhibiting the resupply of nutrients to the surface and by shadowing of silts contained in the meltwater. Finally, the POC flux close to glacier fronts was enhanced due to ballasting by silts, which diminished the remineralisation within the water column and increased the share of organic carbon that reached the sea floor. In Outer Scoresby Sund, by contrast, most remineralisation took place in the upper water column and particle concentrations below were mainly dependent on the present water mass. This study presents the first findings ever about biogeochemical cycling in Scoresby Sund. The results imply that Greenland fjords should be examined on a regional scale to highlight significant differences in carbon dynamics depending on the degree of meltwater discharge within a single fjord system.