The variability of the freshwater export through the Canadian Arctic Archipelago (CAA) is analyzed using a hindcast simulation forced by surface atmospheric forcing from the ERA40 reanalysis (1958–2001). Although the two channels representing the archipelago in the model are both sensitive to the along-channel sea surface height (SSH) gradient, they appear to have very distinct behaviors. The outflow to Lancaster Sound is shown to be largely controlled by the magnitude of the upstream SSH gradient across McClure Strait. The gradient shows a close link to the wind stress curl in the western Arctic but also to a large-scale SSH anomaly pattern which has a strong signal over the shelf to the south of McClure Strait. The latter has, however, little statistical connection to the SSH variability in the Beaufort Gyre. By contrast, the outflow through Nares Strait responds preferentially to SSH variations in the northern Baffin Bay which are remotely forced by air-sea heat exchanges in the Labrador Sea. The variability is largely coherent between the two outflows and is controlled by a dipolar atmospheric pattern reminiscent of the North Atlantic/Arctic Oscillation. When entering the subpolar gyre, the CAA freshwater outflow remains confined to the Labrador shelf with little impact on the salinity of the interior Labrador Sea and potentially on the convection. The latter is represented by a distinct mode of salinity variability in the western subpolar gyre which is rather influenced by the variability of the sea ice export through Fram Strait.