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 Last Interglacial (Eemian Stage, Late Pleistocene). Warm, saline waters (ca. 10–15 psu) entered the site from the North Sea within the first few hundred years of the Eemian, corresponding to the Pinus–Betula (E1) or Pinus–Betula–Ulmus (E2) regional pollen assemblage zones (RPAZ). By about 300 years (beginning of RPAZ E3), dinoflagellate cyst assemblages were already indicating summer sea-surface salinities in excess of about 15 psu and temperatures that perhaps exceeded 27°C. 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 appears to correspond to an opening of the Danish Belts. There is little if any evidence of arctic waters throughout the sequence. 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 (E5) RPAZ 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, and reveals a flora with distinctive Lusitanian/Mediterranean affinities.