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Human impacts on Earth's atmosphere, hydrosphere, litosphere and biosphere are so significant as to naming a new geological epoch, the Anthropocene. Lakes and their biota are highly sensitive to environmental changes. Among aquatic organisms, microbial eukaryotes play fundamental roles associated with lake ecosystem functioning, food webs, nutrient cycling, and pollutant degradation. However, the response of lake microbial eukaryotic community during the Anthropocene to changes in environmental conditions remain poorly understood. Here, we applied a 18S metabarcoding approach to sedimentary DNA to reconstruct the temporal dynamics of microbial eukaryotic community over the past 160 years. We investigated the influence of environmental conditions and of biotic interactions on the microbial eukaryotes in Sihailongwan Maar Lake, one of the candidate sites of Global boundary Stratotype Section and Point (GSSP) for demarcation of the Anthropocene. Microbial eukaryotes were dominated by dinoflagellates, chlorophytes, ciliates, pirsoniales, rotifers, ochrophytes, apicomplexans and cercozoans that were divided into four functional groups that are photoautotrophs, mixotrophs, consumers and parasites. The predominance of phototrophs and their strong associations with organisms from other trophic levels, confirmed their crucial roles in nutrient cycling, energy flows and ecosystem services in freshwater ecosystems. Abrupt changes in the 1950s in microbial eukaryotic diversity and composition were consistent with changes observed in the pollutants emissions i.e., heavy metals, combustion indices (spheroidal carbonaceous particles, polycyclic aromatic hydrocarbon, Soot F14C), radioactivity indicators (239,240Pu, 129I/127I), nutrients (total organic carbon, total nitrogen, phosphorus), and temperature. Statistical analysis revealed that anthropogenic drivers controlled the temporal dynamic of microbial eukaryotic community. Our findings provide additional biostratigraphy evidence of the impact of environmental change on this lake biota, which further supports the value of this system to characterize the Anthropocene.