A reconstruction of oceanographic variability of the past 5800 years on the southeast Greenland shelf was obtained by analysing a combined marine sediment record based on two cores from the same site. Cores Fox04G/05R were retrieved from a side basin to a cross-shelf trough connecting the 900 m deep Sermilik Fjord with the Irminger Sea in the northwestern North Atlantic. The record was analysed in terms of grain size distribution, XRF and benthic and planktonic foraminiferal content and the chronology was obtained on the basis of 210Pb and 14C dating. The late-Holocene paleoceanographic variations in the record were characterised by a marked influence from the Irminger Current (IC) at the onset of the record at 5800 cal. yr BP and the regional Holocene Climatic Optimum between 5200 and 4200 cal. yr BP. After 3600 cal. yr BP Neoglacial cooling with increased influence of polar waters from the East Greenland Current (EGC) diminished the influence from the IC. Between 1500 and 700 cal. yr BP, the environment was highly dominated by cold low-salinity water masses characterised by sea ice forming locally and/or transported with an intensified EGC. At 700 cal. yr BP, concordant with the onset of the 'Little Ice Age', inflow of IC water masses intensified, notably during short-lived warming episodes of the North Atlantic Current most likely related to a contracted subpolar gyre. At the same time, the EGC polar water transport also intensified leading to a stratified water column on the shelf and this may have favoured entrainment of warm subsurface IC waters. Alternatively, the relatively warm rim of the eastern subpolar gyre may have promoted intense submarine melting of extended Southeast Greenland outlet glaciers at this time, producing enhanced meltwater outflow which favoured estuarine circulation processes maintaining the inflow of IC water masses.