Absorption coefficients of colored dissolved organic matter (CDOM) were measured together with salinity, δ18O, and inorganic nutrients across the Fram Strait. A pronounced CDOM absorption maximum between 30 and 120 m depth was associated with river and sea ice brine enriched water, characteristic of the Arctic mixed layer and upper halocline waters in the East Greenland Current (EGC). The lowest CDOM concentrations were found in the Atlantic inflow. We show that the salinity-CDOM relationship is not suitable for evaluating conservative mixing of CDOM. The strong correlation between meteoric water and CDOM is indicative of the riverine/terrigenous origin of CDOM in the EGC. Based on CDOM absorption in Polar Water and comparison with an Arctic river discharge weighted mean, we estimate that a 49–59% integrated loss of CDOM absorption across 250–600 nm has occurred. A preferential removal of absorption at longer wavelengths reflects the loss of high molecular weight material. In contrast, CDOM fluxes through the Fram Strait using September velocity fields from a high-resolution ocean–sea ice model indicate that the net southward transport of terrigenous CDOM through the Fram Strait equals up to 50% of the total riverine CDOM input; this suggests that the Fram Strait export is a major sink of CDOM. These contrasting results indicate that we have to constrain the (C)DOM budgets for the Arctic Ocean much better and examine uncertainties related to using tracers to assess conservative mixing in polar waters.