This paper discusses the results of siliceous microfossils studies performed in a “staircase” of four isolation basins (33.7 m–2.9 m a.s.l.) on Big Solovetskiy Island (Solovki Archipelago, the White Sea). Diatoms were used as a primary group for paleoinferences, while chrysophyte cysts and sponge spicules also demonstrated high indicative potential. In all study lakes, the siliceous microfossils stratigraphy revealed three main stages of their evolution, i.e. large-basin, transitional and small-lake stages, each characterized by certain composition of the diatom assemblages and floristic diversity, relative abundances of chrysophyte cysts and sponge spicules, and siliceous microfossils concentrations. In the uppermost lake, glaciolacustrine environments unfavorable for aquatic biota existed during the large-basin stage. The proglacial lake stage terminated prior to ca. 10.4 cal ka BP, followed by a (semi)terrestrial episode before the transition to small-lake environments. In the other three lakes, marine environments were inferred at the earlier stage, characterized by the predominance of marine and brackish-marine diatoms, increased proportions of sponge spicules and low “cysts to diatoms” ratio. At the transitional marine-freshwater stage, mass growth of small fragilarioid diatoms and decreased abundances of spicules indicated unstable environments, while increased proportions of cysts pointed to progressive freshening of the basins. The duration of the marine-freshwater transition expectedly prolonged from ca. 200 yr in the upper basin (16.6 m a.s.l) to ca. 500 yr in the lowermost lake (2.9 m a.s.l.). The isolation from the sea took place between ca. 6.3 and 1.4 cal ka BP. At the small-lake stage, siliceous microfossils stratigraphies reflected local specifics of the basins and their catchments. We argue that besides traditionally used diatom data, relative and absolute abundances of siliceous microfossils also possess high indicative value for isolation basin studies. Our study demonstrated that marine waters on Big Solovetskiy Island never reached ca. 34 m a.s.l. during the Holocene, unlike the western coast of the Onega Bay where the Preboreal marine intrusion was recorded even at higher elevated localities. Different rates and amplitudes of shoreline displacement are thus suggested for the inner and outer parts of the Onega Bay. During the mid-Holocene Tapes transgression, before ca. 6.3 cal ka BP, the relative sea level on Big Solovetskiy Island exceeded 17 m a.s.l. The average estimated rates of the shoreline retreat during the second half of the Holocene gradually decreased from 0.28 cm year−1 to 0.2 cm year−1, indicating slowed isostatic uplift.