<p>The vast territory of the West Siberian Plain encompasses a multitude of lakes, rivers, and swamps. These aquatic environments are impacted by current climate changes, including increases in water temperature and mineralization, which in turn lead to changes in the composition of their microbial communities. The 16S rRNA gene metabarcoding technology was used to study the taxonomic composition and functional potential of bacterioplankton from 20 lakes in the forest–swamp and forest–steppe natural zones of the West Siberian Plain. The bacterioplankton of forest–steppe lakes demonstrated higher richness and diversity, a more complex structure and a greater functional potential compared to the bacterioplankton of forest–swamp lakes. Water pH and mineralization played an important role in the distribution of dominant bacterial taxa and the formation of community composition. Azonal factors had a significant impact also, and, first, the input of soil bacteria into the lake from the catchment area. These soil bacteria significantly transformed the lake community composition and could act as keystone taxa. The brackish forest–steppe Lake Solenoye and the littoral zone of the freshwater forest–swamp Lake Chertankul, characterized by low temperature and pH, differed the most in terms of bacterioplankton composition from the other lakes studied. Methane-oxidizing bacteria were detected in all lakes, but the highest proportion of orthologous gene groups involved in methane oxidation was found in the littoral zone of Lake Chertankul. The data obtained can be useful for predicting the responses of lake microbial communities to climate changes and their consequences.</p>