The research on mountain lakes located in non-industrialised areas provides a thorough look at the background condition of the communities of hydrobionts in terms of their composition, structure, and distribution. Lake Shebety is a glacial moraine lake of the Baikal Lake basin, Russia that could be used as a pattern for studying biodiversity and adaptive mechanisms of aquatic communities. This paper is aimed to identify the essential transient factors that regulate the composition and structure of phytoplankton and zooplankton in different zones of Lake Shebety. This will provide a better understanding of the plankton dynamics under the extreme continental climate. The present article is the first limnological investigation conducted for the water body on the above mentioned factors. Samples were collected during the summer of 2002 and 2016. Lake Shebety is located at 1567.4 m above sea level in the Khentei-Daurian Highland which lies in the Chikoi National Park, Trans-Baikalsky Krai, Russia. The research was performed on the basin morphometry and hydrochemical composition, along with hydrobiological studies of phytoplankton and zooplankton. Typical ecosystem features include oligotrophic status, low salinity, and high oxygen content. The lake is mainly characterised by deep-water areas with shallow-water shorelines. The study covers environmental factors determining the distribution and development of plankton communities in a mountain deep-water lake under extreme continental climate condition. We have detected a total of 35 algae species belonging to the following phyla: Cyanobacteria, Bacillariophyta, Cryptophyta, Chrysophyta, Dinophyta, Chlorophyta, and Charophyta. The data on zooplankton consisted of 35 species representing the phyla of Rotifera, Cladocera, and Copepoda. The greatest diversity of species was observed for the diatoms and cladocerans. It is apparent that the geographical distribution of some species of rotifers and crustaceans has been expanded. The species of Euchlanis alata, Acantocyclops capillatus, and Cyclops abyssorum are rare species for the water bodies in the Trans-Baikalsky Krai. The littoral plankton community is more diverse in components and quantities as compared to the pelagic one. As per the CCorA, the factors that contribute to the abundance and biomass of Bacillariophyta, Chlorophyta, Chrysophyta, Dinophyta, Rotifera, Cladocera, and Copepoda have been observed in the following descending order: depth, phosphorus content, water temperature, and pH in littoral zone; pH, color, turbidity, nitrogen content determine density of Bacillariophyta, Chlorophyta and Copepoda in the pelagic zone. The abundance of alga Crucigeniella irregularis and rotifers Kellicottia longispina and Conochilus unicornis were positively related to the phosphate content in the shallow areas. The abundance of the phytoplankton species Kephyrion doliolum, Cryptomonas ovata, Crucigenia tetrapedia, Peridinium sp. and zooplankton species Arctodiaptomus neithammeri and Cyclops abyssorum are associated with chem...