A rich organic-walled dinoflagellate cyst and pollen record from the Licze borehole in northern Poland has been used to reconstruct the hydrographic history of the southeastern Baltic Sea during the Eemian Stage (Last Interglacial) of the Upper Pleistocene. Warm and saline waters (ca. 10–15 psu) entered the site within the first few hundred years of the Eemian, and by about 300 years, dinoflagellate cyst assemblages were already indicating salinities in excess of about 15 psu and summer temperatures that perhaps exceeded 27°C. A North Sea source is indicated, with little if any influence of arctic waters. Warm and saline conditions of 15–20 psu or more, at least twice present levels, persisted throughout the early Eemian. A rise in sea level at Licze appears to correlate with a similar event in eastern Denmark, as both coincide with the increase in Corylus (ca. 750 years into the interglacial). This sea-level rise might therefore have a basinwide extent, and has been attributed to an opening of the Danish Belts. Whereas dinoflagellate cysts reflect sustained high salinites within the upper water column, a concomitant increase in abundance of the chlorococcalean alga Pediastrum within the Carpinus–Corylus–Alnus regional pollen assemblage zone (RPAZ) E5 indicates an escalating freshwater input, presumably from the proto-Vistula whose mouth was nearby. This suggests the development of a thin, seasonal, low-salinity surface layer below which dinoflagellates lived in more saline waters. Increasing fluvial influence suggests shallowing through RPAZ E5. This study is the first to document dinoflagellate cysts from the Eemian of the southeastern Baltic Sea. Most species have not been reported previously from either Eemian or Holocene sediments of the Baltic Sea proper.