Fossil marine diatom assemblages in a sediment core from the central northern Faroe slope in the Norwegian Sea were used to reconstruct palaeoceanographic changes in the surface water mixed layer from the last ~130,000 years (Marine Isotope Stage (MIS) 6/5 transition to MIS 1 (including the Eemian and Holocene interglacials) and to compare the results with previously published results on planktic foraminifera representing the subsurface conditions of the thermocline. Diatom floras from MIS 5 of the Nordic seas have rarely been studied in detail before and never the entire period from pre-Eemian to present. The composition of diatom species together with maxima in absolute abundance of diatoms, indicate two periods of warmer sea surface temperatures correlating with the Eemian and Holocene interglacials, respectively. The Eemian differs from the Holocene in that the Iceland-Faroe Front never developed, suggesting the cold East Icelandic Current (originating from the East Greenland Current) running north of Iceland was reduced or more mixed with Atlantic water than during the Holocene and that the surface temperature and salinity gradients were weaker. The northern Faroe slope was in the early Weichselian of MIS 5d–5a mainly influenced by weaker inflow of Atlantic water and stronger influence of the East Icelandic Current and by seasonal sea-ice cover. During the later part of the Weichselian (MIS 4–MIS 2) cold conditions prevailed with extensive sea-ice cover except during the warmer interstadials. The diatom floras were more sensitive to climate changes than the planktic foraminifera and indicate longer periods with warm surface conditions, and increased influence of the warm Atlantic surface water from the Faroe Current in MIS 5, suggesting a shallower and much steeper thermocline during the transitional periods compared to today. The diatoms are good indicators for Atlantic water inflow and possible convection in the Nordic seas, not merely reflecting orbital variations in insolation as previously suggested.