Five stages of development of the Vistula Lagoon were established based on the diatom flora preserved in 6 sediment cores. The study shows that the area originally had a terrestrial environment, whereas its later evolution is linked with the marine stages of the Baltic Sea. As a result of input of marine waters through the Vistula Spit, which is indirectly connected to Litorina transgressions, the shallow, eutrophic, brackish-water basin originated. In the next stage decrease in water level and salinity are noted. Moreover, symptoms of the Post-Litorina transgression were observed in the diatom record. Finally, the effects of the eutrophication are recorded in subfossil diatom flora. As a consequence of closing of the Nogat River inflow, the stronger influence of marine waters from the Baltic Sea are observed in the lagoon.