Lake ecosystems are affected globally by climate warming and anthropogenic influences. However, impacts on boreal lake ecosystems in eastern Siberia remain underexplored. Our aim is to determine if shifts in diatom assemblages in a remote lake in eastern Siberia are related to climate warming, similar to observations in temperate regions, while also exploring how the ecosystem might be influenced by hydroclimate and human-induced air pollution. We analysed continuous sediment samples from a 210Pb–137Cs-dated short core from Lake Khamra (59.99° N, 112.98° E), covering ∼220 years (ca. 1790–2015 CE), following a multiproxy approach on the same sample material to provide a comprehensive record of environmental changes. Biogeochemical proxies include total organic carbon (TOC) and total nitrogen (TN) concentrations and corresponding stable isotopes of bulk sediment samples (δ13C, δ15N), as well as diatom silicon isotopes (δ30Sidiatom), alongside light microscope diatom species analysis. The diatom assemblage at Lake Khamra is dominated by few planktonic species, primarily Aulacoseira subarctica and Aulacoseira ambigua. At ca. 1970 CE, we observe a major shift in diatom assemblages, characterised by a marked increase in the planktonic species Discostella stelligera and a decrease in both Aulacoseira taxa. We attribute these changes to recent global warming, which is likely associated with earlier ice-out and enhanced summer thermal stratification, consistent with similar observations in temperate lake ecosystems. A rapid increase in chrysophyte scales (Mallomonas) from the 1990s onward further supports an increasing thermal stratification of the lake driven by rising temperatures. Biogeochemical proxies indicate substantial limnological changes around 1950 CE, preceding the major shift in diatom communities, likely driven by hydroclimatic variability. Increased precipitation and weathering are further discussed in order to explain changing silica sources leading to decreasing δ30Sidiatom after ∼1970 CE. Nevertheless, the interpretation of δ30Sidiatom in lacustrine systems is complex, likely influenced by both in-lake biogeochemical processes and catchment dynamics. Indications of anthropogenic influences on Lake Khamra include a δ13C depletion, likely linked to fossil fuel combustion and emissions, coinciding with industrial growth in Asia and Russia. Nonetheless, we find no evidence for atmospheric nitrogen deposition. We conclude that the Lake Khamra ecosystem is severely affected by climate warming and shows indications of human influence. This emphasises the urgent need for comprehensive research to mitigate these impacts on remote lake ecosystems in order to secure natural water resources.