A high-resolution multiproxy study of core MD99-2286 reveals a highly variable hydrographic environment in the Skagerrak from 9300 cal. yr BP to the present. The study includes foraminiferal faunas, stable isotopes and sedimentary parameters, as well as temperature and salinity reconstructions of a c. 29 m long radiocarbon-dated core record. The multivariate technique fuzzy c-means was applied to the foraminiferal counts, and it was extremely valuable in defining subtle heterogeneities in the foraminiferal faunal data corresponding to hydrographic changes. The major early-/mid-Holocene (Littorina) transgression led to flooding of large former land areas in the North Sea, the opening of the English Channel and Danish straits, and initiation of the modern circulation system. This is reflected by fluctuating C/N values and an explosive bloom of Hyalinea balthica. A slight indication of ameliorated conditions between 8000 and 5750 cal. yr BP is related to the Holocene Thermal Maximum. A subsequent increase in freshwater/Baltic water influence between 5750 and 4350 cal. yr BP is reflected by dominance of Bulimina marginata and depleted delta O-18 values. The Neoglacial cooling (after 4350 cal. yr BP) is seen in the Skagerrak as enhanced turbidity, increasing TOC values and short-term changes in an overall Cassidulina laevigata-dominated fauna suggesting a prevailing influence of Atlantic waters. This is in agreement with increased strength of westerly winds, as recorded for this period. The last 2000 years were also dominated by Atlantic Water conditions with generally abundant nutrient supply. However, during warm periods, particularly the 'Medieval Warm Period'and the modern warming, the area was subject to a restriction in the supply of nutrients and/or the nutrient supply had a more refractory character.