While the influence of the subpolar gyre (SPG) on thermohaline variability in the eastern North Atlantic is well documented, the extent and timescale of the influence of the SPG on North Sea is not well understood. This is primarily because earlier investigations on the causes of variability in the North Sea water properties mostly focused on the role of atmosphere and deployed regional models. Here using a historical simulation with the Max Planck Institute Earth System Model (MPI-ESM), we investigate circulation and water mass variability in key regions, namely, the Rockall Trough and the Faroe-Scotland Channel, which link the North Atlantic to the North Sea. We find that salinity covaries with advective lags in these three regions and that the northern North Sea salinity follows the Rockall Trough with a lag of 1 year. We show that recurring and persistent excursions of salinity anomalies into the northern North Sea are related to the SPG strength and not to the local acceleration of the inflow. Furthermore, we illustrate that the SPG signal is more pronounced in salinity than in temperature and that this simulated SPG signal has a period of 30–40 years. Overall, our study suggests that, at low frequency, water mass variability originating in the North Atlantic dominates changes in the North Sea water properties over those due to local wind-driven volume transport.