Analyses of sea surface height (SSH) records based on satellite altimeter data and hydrographic properties have suggested a considerable weakening of the North Atlantic subpolar gyre during the 1990s. Here we report hindcast simulations with high-resolution ocean circulation models that demonstrate a close correspondence of the SSH changes with the volume transport of the boundary current system in the Labrador Sea. The 1990s-decline, of about 15% of the long-term mean, appears as part of a decadal variability of the gyre transport driven by changes in both heat flux and wind stress associated with the North Atlantic Oscillation (NAO). The changes in the subpolar gyre, as manifested in the deep western boundary current off Labrador, reverberate in the strength of the meridional overturning circulation (MOC) in the subtropical North Atlantic, suggesting the potential of a subpolar transport index as an element of a MOC monitoring system.