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The accelerating melt of the Greenland Ice Sheet is releasing large volumes of freshwater into the coastal ocean, diluting seawater alkalinity. Biogeochemical processes such as photosynthesis, respiration, and sediment mineral dissolution also shape carbon dynamics in these freshened waters, but their combined influence on the ocean’s carbon pump remains unresolved. Here we isolate the chemical effects of meltwater dilution through a controlled seawater-freshwater mixing experiment, providing empirical evidence for nonlinear reduction in the partial pressure of carbon dioxide (pCO2). Carbonate system modeling revealed the mechanisms behind this nonlinearity, helping to explain 17 years of low pCO2 in a Greenlandic fjord. Sensitivity analysis shows that the influence of biogeochemical processes is fundamentally shaped by the chemical environment in which they operate. Freshwater input reduces buffering capacity and therefore amplifies the system’s sensitivity to biological activity and acidification. Our findings highlight how meltwater amplifies biogeochemical control of pCO2 in Arctic coastal systems.