New data, obtained by studying the composition of the diatom complexes in the top-core sediments from eight lakes in Zaonezhye located at different absolute altitudes above sea level, are reported. The evolutionary conditions for the diatom flora were assessed, and the water mineralization of the lakes, acidity of the medium and climatic variation trends in the modern era were reconstructed. The water mineralization of the lakes was found to be directly related to the type of the crystalline bedrock, the composition of Quaternary deposits, the size and depth of the lakes, and their position in fault zones. The diatom complexes evidence a directed climatic warming trend indicated by a decline or even vanishing of arctalpine forms and a greater variety of boreal forms and cospopolites. Dominant species were identified to reveal similarities and differences in the evolution of the lakes, preliminary conclusions regarding the timing of their detachment from the periglacial Lake Onega (PLO) were drawn, and variations in its water level in the Late Glacial and the Holocene are shown.