Early to late Holocene sediments from core F80, Fårö Deep, Baltic Sea, are investigated for their palynomorph composition and dinoflagellate cyst record to map variations in sea-surface-water salinity and palaeoproductivity during the past 6000 years. The F80 palynomorph assemblages are subdivided into four Assemblage Zones (AZs) named A to D. The transition from the stratigraphically oldest AZ A to B reflects a marked increase in palaeoproductivity and a gradual increase in surface-water salinity over the ∼1500 years between the Initial Littorina (former Mastogloia Sea Stage) and Littorina Sea Stage. A period with maximum sea-surface salinity is recorded within the overlying AZ C from 7200 to 5200 cal. a BP, where the process length of Operculodinium centrocarpum indicates that average salinities were probably the highest (∼15–17 versus 7.5 psu today) since the last glaciation. The change from AZ C to D correlates with a shift from laminated to non-laminated sediments, and the dinoflagellate cyst assemblages suggest that the surface- and the deep-water environment altered from c. 5250 cal. a BP, with less productivity in the surface water and more oxygenated conditions in the deep water. Here we demonstrate that past regional changes in surface salinity, primary productivity and deep-water oxygenation status in the Baltic Sea can be traced by mapping overall palynomorph composition, dinoflagellate cyst assemblages and variations in the process length of O. centrocarpum in relation to periods of laminated/non-laminated sedimentation and proportion of organic-matter in the sediments. An understanding of past productivity changes is particularly important to better understand present-day environmental changes within the Baltic Sea region.