Dinoflagellate cysts were used as a proxy for reconstructing the salinity variations during the Holocene in the southwestern Black Sea. The aim of this study was to determine the timing of the reconnection between the Black and Marmara seas. Core GeoB 7625-2, located 50 km northeast of the mouth of the Sakarya River, was sampled with a 200-year resolution between 7.42 and 0.52 ka BP. The lower part of the core was sampled with varying resolution. A distinct change in the dinoflagellate cyst assemblages from freshwater/brackish water to saltwater was observed between ~ 8.25 and ~ 7.97 ka BP, which is ~ 0.6 ka earlier than observed in other dinoflagellate cyst studies. This discrepancy may indicate the diachronous salinification of the Black Sea. The freshwater to brackish water assemblage is dominated by Pyxidinopsis psilata and Spiniferites cruciformis, while the most important euryhaline species are Lingulodinium machaerophorum and cysts of Pentapharsodinium dalei. The average process length of Lingulodinium machaerophorum was used as a salinity proxy. Both proxies suggest a gradual reconnection between the Black and Marmara seas, and these findings confirm earlier studies. Peridinium ponticum is restricted to the Black Sea; abundance fluctuations of this species were controlled by salinity variations and changes in nutrient concentrations. Earlier studies have demonstrated that the 800 to 500 year cycles observed in the sedimentary record are related to the intensity of the discharge of the Sakarya River, and linked to the North Atlantic Oscillations. Cysts of Pentapharsodinium dalei and Spiniferites spp. fluctuated synchronously with the clay layer frequency. The poor preservation of these forms may indicate shelfal transport during periods of intense river discharge. The variation in relative abundance of heterotrophic species does not correlate with the clay layer frequency, since upwelling and nutrient supply also influenced their abundances. Lingulodinium machaerophorum shows the highest relative abundances during periods with reduced river input.