Abstract The rapid deglaciation of the Arctic increases the flux of terrestrial organic matter into the marine carbon cycle. The proportions, mixing, and turnover rates of organic matter from deglaciated terrestrial and glacial watershed sources are poorly understood in Arctic fjords. We characterized the mixing and flux of dissolved organic matter (DOM) in two Arctic fjords, Kongsfjorden and Scoresby Sund. DOM was sampled and analyzed along the natural mixing gradient from glacial meltwater to the marine waterbody to reveal chemical proxies for glacier‐derived organic matter utilizing (ultra)high‐resolution mass spectrometry of solid‐phase extracted DOM. The molecular composition of DOM in Kongsfjorden was homogenous in elemental ratios of O/C, H/C, and N/C and aromaticity due to high mixing and low glacial run‐off. In Scoresby Sund, a strong correlation between DOM composition and salinity was observed. The freshwater proportion of DOM was characterized by a low N/C ratio, unsaturated molecules, and a high terrestrial index. The surface stratification in Scoresby Sund prevented vertical mixing of glacier‐derived and marine DOM with denser water masses. Glacial meltwater DOM in Scoresby Sund was similar to terrestrial DOM, suggesting either an unknown source of additional DOM or selective DOM removal processes. In summary, the high proportion of terrestrial DOM proxies suggests a strong imprint of deglaciation on the Arctic carbon cycle.