Description: Key Points In Kongsfjorden, an Arctic glacier fjord, freshwater from glacier runoff and ice meltwater decreases phosphate, alkalinity and DOM concentrations Estuarine mixing is the major driver of summer CO2 undersaturation in glacially modified waters and near‐corrosive conditions were observed Future changes will amplify ocean acidification in the inner‐fjord surface waters Abstract A detailed survey of a high Arctic glacier fjord (Kongsfjorden, Svalbard) was carried out in summer 2016, close to the peak of the meltwater season, in order to identify the effects of glacier runoff on nutrient distributions and the carbonate system. Short‐term weather patterns were found to exert a strong influence on freshwater content within the fjord. Freshwater inputs from glacier runoff and ice meltwater averaged (±SD) low nitrate (1.85±0.47 μM; 0.41±0.99 μM), orthophosphate (0.07±0.27 μM; 0.02 ±0.03 μM), dissolved organic carbon (27 ±14 μM in glacier runoff), total alkalinity (708±251 μmol kg‐1; 173±121 μmol kg‐1) and dissolved inorganic carbon (622±108 μmol kg‐1; 41±88 μmol kg‐1), as well as a modest silicate concentration (3.71±0.02 μM; 3.16±5.41 μM). pCO2 showed a non‐conservative behavior across the estuarine salinity gradient with a pronounced under‐saturation in the inner‐fjord, leading to strong CO2 uptake from the atmosphere. The combined effect of freshwater dilution and atmospheric CO2 absorption was the lowering of aragonite saturation state, to values that are known to negatively affect marine calcifiers (ΩAr, 1.07). Glacier discharge was therefore a strong local amplifier of ocean acidification. Future increases in discharge volume and the loss of marine productivity following the retreat of marine‐terminating glaciers inland are both anticipated to further lower ΩAr within inner‐fjord surface waters. This shift may be partially buffered by an increase in the mean freshwater total alkalinity as the fractional importance of iceberg melt to freshwater fjord inputs declines and runoff increases.