Seismic profiles and mollusks have been used to suggest that from ∼12 500 to 7000 yr BP, the Black Sea was an isolated freshwater lake containing potable water and implying a surface salinity of <1. According to Ryan and Pitman (1999), these circumstances encouraged Neolithic settlement and farming on the shore of the Black Sea. This model conflicts with previous studies of dinoflagellate cysts and seismic profiles from the Marmara Sea. Here we investigate Ryan and Pittman’s model using palynological studies of organic-walled dinoflagellate cysts, acritarchs, freshwater algae, microforaminifera, and fungal remains as tracers of changes in surface salinity for seven cores of pleniglacial to Holocene sediments from the Marmara and Black seas. Core-top data from 16 sites along a salinity gradient from 39.5 in the Aegean Sea to ∼17 in the Black Sea show that the dinocyst species Impagidinium aculeatum, Impagidinium patulum, Operculodinium israelianum, Polysphaeridium zoharyi and Nematosphaeropsis labyrinthus are markers of Mediterranean Sea water and summer surface salinity >24, and that Spiniferites cruciformis, Spiniferites inaequalis, Peridinium ponticum, Polykrikos spp. and Quinquecuspis concreta characterize the lower salinity of the Marmara and/or Black seas. The core-top data and correlatable down-core assemblage changes in time-equivalent sapropelic and brown muds show that there is no evidence for differential aerobic decay of dinocysts in the study area. The main acritarchs are Sigmopollis psilatum, Concentricystes cf. C. rubinus and cf. Acritarch-8 of Traverse (1978), all of which are absent from the Aegean Sea and decrease in abundance with increasing salinity; the first two taxa have been reported previously as freshwater species. Fungal remains show a similar distribution pattern to the freshwater acritarchs, indicating their origin from terrestrial environments. Freshwater Chlorococcales are almost confined to the Black Sea but they have rare occurrences in the Aegean, indicating long-distance transport. Microforaminiferal linings are abundant in the Marmara Sea but are absent in deep water of the Black Sea. In the Marmara Sea, mid–late Holocene assemblages (<7 ka) are dominated by Lingulodinium machaerophorum, Operculodinium centrocarpum and halophilic Mediterranean Spiniferites spp. ( S. mirabilis, S. hyperacanthus, S. bentorii), and a diversity of heterotrophic protoperidinioid and Polykrikos species are present in both sapropels and brown lutites. In contrast, the early Holocene interval (including sapropels) has fewer halophilic Spiniferites spp. and other Mediterranean taxa ( O. israelianum, Polysphaeridium zoharyi) and more low salinity indicators ( P. ponticum, Pyxidinopsis psilata and S. cruciformis), suggesting that the overflow of Black Sea water was greater than now. The time-equivalent early Holocene unit in the Black Sea has a higher percentage of taxa found in freshwater environments (including S. cruciformis forms 1–3; Gonyaulax apiculata, fungal remains and freshwater acritarchs) but the continued presence of Spiniferites morphotypes and other taxa associated with brackish (∼7–18) to saline surface water indicates that there was some Mediterranean water present at this time. The late glacial and Pleniglacial sediments in the Marmara Sea contain a lower diversity of dinoflagellates, dominated by S. cruciformis and P. psilata, as in early Holocene sediments of the Black Sea but including the short-spine morphotypes of S. cruciformis which are not found in freshwater lakes. We conclude that although the glacial stages were marked by much lower sea-surface temperatures, there was either some periodic marine influence or the marine dinocysts were living in a brackish water environment (∼7–18) with the freshwater species being transported from glacial lakes. Overall, there is no palynological evidence that the surface salinity of the Black or Marmara seas was ever as low as a freshwater lake. This finding is consistent with models that estimate the time required to desalinate the Black Sea after closing of the Marmara–Bosphorus gateway.