Global warming accelerates melting of glaciers and increases the supply of meltwater and associated inorganic particles, nutrients, and organic matter to adjacent coastal seas, but the ecosystem impact is poorly resolved and quantified. When meltwater is delivered by glacial rivers, the potential impact could be a reduction in light and nutrient availability for primary producers while supplying allochthonous carbon for heterotrophic processes, thereby tipping the net community metabolism toward heterotrophy. To test this hypothesis, we determined physical and biogeochemical parameters along a 110-km fjord transect in NE Greenland fjord, impacted by glacial meltwater from the Greenland Ice Sheet. The meltwater is delivered from glacier-fed river outlets in the inner parts of the fjord, creating a gradient in salinity and turbidity. The planktonic primary production was low, 20–45 mg C m⁻² d⁻¹, in the more turbid innerhalf of the fjord, increasing 10-fold to around 350 mg C m⁻² d ⁻¹ in the shelf waters outside the fjord. Plankton community metabolism was measured at three stations, which displayed a transition from net heterotrophy in the inner fjord to net autotrophy in the coastal shelf waters. Respiration was significantly correlated to turbidity, with a 10-fold increase in the inner turbid part of the fjord. We estimated the changes in meltwater input and sea ice coverage in the area for the last 60 y. The long-term trend and the observed effects demonstrated the importance of freshwater runoff as a key driver of coastal ecosystem change in the Arctic with potential negative consequences for coastal productivity.