During an east-to-west transect through the Canadian Arctic Archipelago, dissolved inorganic carbon (DIC) and total alkalinity (TA) were measured. The watermass composition throughout the Archipelago is determined using TA and the seawater oxygen isotope fractionation (δ18O) data, and the carbon characteristics of these waters are examined. The influence of the Mackenzie River is primarily limited to the upper water column in the western Archipelago while the fraction of sea-ice melt water in the surface waters increases eastward with maximum values at the outflows of Jones and Lancaster Sounds. The depth of Pacific-origin upper halocline waters increases eastward through the Archipelago. In the western Archipelago, non-conservative variations in deep water DIC are used to compute a subsurface carbon surplus, which appears to be fueled by organic matter produced in the surface layer and by benthic respiration. The eastward transport of carbon from the Pacific, via the Arctic Archipelago, to the North Atlantic is estimated, and the impact of increased export of sea-ice melt water to the North Atlantic is discussed.