A sedimentary diatom record of Lake Goluboye, Karelian Isthmus (NW Russia) revealed two transgressive stages of the Baltic: the Ancylus Lake and the Litorina Sea, followed by two “small-lake” stages. During the Ancylus Lake transgression, a shallow bay of the Ancylus Lake existed in the Lake Goluboye basin, and species-rich benthic-dominated diatom assemblages formed in oligotrophic, low-mineralisation environments. The isolation from the Ancylus basin took place after ca. 9800 cal. yrs BP, when a small nutrient-rich lake formed in the basin. Two Litorina Sea transgressive phases were inferred from the diatom record of Lake Goluboye, both characterised with similar low-salinity environments. Such a weak signal of the marine transgression, compared with the other coastal sites in the Karelian Isthmus, might have resulted from the sheltered position of the lake. Our data also suppose that the maximum transgression level in the study area was lower than has previously been suggested. With the termination of the Litorina transgression shallow-water conditions with extensive macrophytes growth was established in the lake. Before ca. 4800 cal. yrs BP nutrient-rich small-lake conditions, similar to the post-Ancylus stage, became established.