Benthic foraminifera and stable isotope data from the last interglaciation (Eemian, substage 5e) from a borehole at Skagen, Denmark, provide evidence for major environmental and hydrographic changes during this period. During the first millennium of the Eemian, water masses covering northern Denmark became gradually warmer. Temperate conditions prevailed during most of the interglaciation, but these were interrupted by two periods with decreased water temperatures. The first cooling (Event S-1) was not very distinct at Skagen, but the second (Event S-2), seen in both the foraminiferal and oxygen isotope record, represents a large shift to subarctic conditions. Carbon isotopes indicate a change in ocean circulation during both events. No comparable climate variations are seen within the Holocene record at the site. The final cooling of the water masses associated with the substage 5e/5d boundary occurred within a few hundred years. These last interglacial climatic changes were probably caused by variations in strength and/or position of the North Atlantic Drift, possibly as a result of varying vigor of the Atlantic conveyor. In addition, minor variations in the fossil assemblages also indicate fluctuations in the inflow of Atlantic water to the Skagerrak–Kattegat area during the warm intervals of substage 5e.