Background Metagenomic analysis was used in this investigation to present the results of the microbiome studies on Aidyn, Brusyanoe, and Rybny Sakryl lakes in the West Kazakhstan region. The technological basis of the research was high-performance Illumina next-generation sequencingResults The sequencing of 36 amplicon libraries yielded at least 20,000 sequences per library, which were subjected to primary taxonomic analysis; 4000 taxons were identified to belong to approximately 400 genera. Results showed that unclassified bacteria, Proteobacteria, Bacteroidota, and Actinobacteriota were dominant. According to the Shannon metric, the samples from Brusyanoe lake had the richest and the most even communities. Subsequently, samples from the Aidyn and Rybny Sakryl lakes, which also had the most even communities according to the Simpson metric. The study also revealed that the taxonomic structure of microbiomes from different lakes had several common features. All samples were characterized by the presence of the following groups of bacteria: Verrucomicrobiae, Gammaproteobacteria and Alphaproteobacteria, Cyanobacteria, Bacteroidia, Actinobacteria, and Acidimicrobiia. Furthermore, comparative analysis of the taxonomic structure of communities showed differences in their structure at the class level as well. Beta-diversity indicated that the taxonomic composition of the communities varied and depended on the sampling location. Weighted Uni Fracmetric, which reflects the similarity in the qualitative composition of the communities, suggested an even taxonomic composition only for the Rybny Sakryllake microbiome. Microbiome samples from Aidyn and Brusyanoe lakes were characterized by the presence of Candidatusaquilinia (2.6–7.5%) and a relatively high content of Algoriphagus (2–8%). Common features between the Aidyn and Rybny Sakryl lake samples included a relatively abundant Methylophilaceae (1.3–3.8%).Conclusion The conducted studies revealed differences in microbiome composition in Aydi, Brusyanoe and Rybny Sakryl lakes.Data analyses revealed that the results of the metagenomic study of the microbiome of inland water bodies can be used as markers to elucidate the ecological state of the lakes examined in the present study. Furthermore, microbial communities adapted to water with significantly high salt contents are predominantly found in the Aidyn lake. However, microbial communities existing in freshwaters with low salt content are typically foundin the Rybny Sakryl and Brusyanoe lakes.