The Arctic Ocean receives a large supply of dissolved organic matter (DOM) from its catchment and shelf sediments, which can be traced across much of the basin’s upper waters. This signature can potentially be used as a tracer. On the shelf, the combination of river discharge and sea-ice formation, modifies water densities and mixing considerably. These waters are a source of the halocline layer that covers much of the Arctic Ocean, but also contain elevated levels of DOM. Here we demonstrate how this can be used as a supplementary tracer and contribute to evaluating ocean circulation in the Arctic. A fraction of the organic compounds that DOM consists of fluoresce and can be measured using in-situ fluorometers. When deployed on autonomous platforms these provide high temporal and spatial resolution measurements over long periods. The results of an analysis of data derived from several Ice Tethered Profilers (ITPs) offer a unique spatial coverage of the distribution of DOM in the surface 800m below Arctic sea-ice. Water mass analysis using temperature, salinity and DOM fluorescence, can clearly distinguish between the contribution of Siberian terrestrial DOM and marine DOM from the Chukchi shelf to the waters of the halocline. The findings offer a new approach to trace the distribution of Pacific waters and its export from the Arctic Ocean. Our results indicate the potential to extend the approach to separate freshwater contributions from, sea-ice melt, riverine discharge and the Pacific Ocean.