The optical properties of chromophoric dissolved organic matter (CDOM) were investigated in the Canadian Archipelago and coastal Beaufort Sea surface waters using fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC). Environmental dynamics of individual components were evaluated and compared to salinity, in situ fluorescence, absorption at 312 nm (a(312)), dissolved organic carbon, and lignin phenol concentrations. A positive linear relationship between four fluorescent components and lignin phenols suggests a terrestrial origin, whereas two components were unrelated to a river source, suggesting an autochthonous source. Elevated concentrations of terrestrial components were observed in the Mackenzie River plume near the coast of Alaska and decreased as water was transported to the Canadian Archipelago. The two nonterrestrial components exhibited only background levels in concentrations along the transect, suggesting minimal productivity within plume and archipelago surface waters. The relative abundance of terrestrial components in relation to nonterrestrial components allowed us to distinguish water masses including Atlantic, Archipelago, and Mackenzie River plume, respectively. This study illustrates the usefulness of PARAFAC to fingerprint water masses based on the optical characteristics of CDOM and shows promise to improve our understanding of upper Arctic Ocean ventilation.