The article considers diatom biostratigraphy and ecological factors of the formation of diatom complexes that characterize the Pleistocene volcanic-sedimentary facies of shelf deposits of the Golovnin Formation. Dividing the Golovnin Formation is proposed according to diatom complexes into three biostratigraphic zones: Zone <i>Eupyxidicula zabelinae,</i> Zone <i>Thalassiosira antiqua</i>, Zone <i>Proboscia Proboscima barboi</i>. Three transgressive phases of formation of the Golovnin deposits were established under the paleoecological analysis of diatom associations. Early Pleistocene transgressions are named Kunashir I (2.12-2.0 Ma) and Kunashiri II (1.95-1.77 Ma). The Late Golovnin transgressions during 0.424-0.374 Ma and 0.337-0.300 Ma are correlated to the Marine Isotopic Stages 11 and 9 respectively.