Preglacial environments in Lake Ladoga, the largest European lake, located within the limits of the Scandinavian glaciations, are very poorly investigated compared to postglacial ones. They were primarily reconstructed based on the studies of terrestrial boreholes and outcrops, often incomplete and poorly dated. Previous diatom studies established that during the Eemian marine transgression, the Ladoga basin became a part of the marine Baltic-White Sea connection. However, the environments established in Lake Ladoga after the regression of the Eemian Sea are not known. This article discusses the first Early Weichselian (MIS5, ~ 118–80 ka) diatom record in Lake Ladoga obtained within the frame of the Russian-German research project PLOT. Low concentrations and selective preservation of diatoms in the preglacial sediments point to unstable high-energy environments. The presence of marine diatoms is thought to result from reworking of marine Eemian sediments, rather than direct marine influence. We argue that post-Eemian environments in Lake Ladoga were neither marine nor glaciolacustrine, as previously suggested. The Early Weichselian diatom record formed in a shallow-water part of a lake affected by inflowing streams transporting large amounts of eroded material. No analogues of the preglacial environments can be found in the postglacial Lake Ladoga. Our record demonstrates close similarity to other Early Weichselian diatom records in the Ladoga region suggesting their formation under the same conditions. Similar trends in concentrations of diatoms, diatom fragments and other siliceous microfossils reflect changing sediment supply, hydrodynamics or reworking intensity. Their lower values ~ 118–113 and ~ 90–80 ka could reflect the Early Weichselian cooling stages, while their increase between ~ 113 and 90 ka might indicate enhanced erosion intensity and increased sediment supply corresponding to the climate amelioration.