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The paper is focused on changes in biodiversity, the environment, and human activity in the Uvs Nuur Basin during the last three millennia based on biological and geochemical proxies from the lake Bayan Nuur. Regions with high biodiversity and relatively low anthropogenic pressures are typically the most vulnerable to both climate change and human activities. One such area is the Uvs Nuur Basin located on the north of the Great Lake Depression of Mongolia. The main objective of this study is to assess changes in the past biodiversity of the lake’s microflora and microfauna, and surrounding vegetation biodiversity in the Uvs Nuur Basin, and to determine the main drivers of diversity change. Based on the analysis of pollen and chironomids we conclude that the most humid and afforested phase was between 1400 and 1800 CE. We assume that the Little Ice Age in the Uvs Nuur Basin was humid with mean annual precipitation ca. 305 mm/year and mean July temperature about 13°C. Conversely, the warmest and most arid period was between 650 and 1350 CE with mean annual precipitation ca. 280 mm/year and mean July temperature of about 16°C, attributed to the Medieval Warm Period. The biodiversity of terrestrial plants, chironomids, and Cladocera positive react to changes in annual precipitation and July temperature, whereas diatoms do not correlate directly to the climatic factors. The diversity and the evenness of plants are strongly correlated with the change in the leading biomes. The calculated species turnover suggests no significant changes in plant and Cladocera taxa composition, but significant changes in diatom and chironomid communities. This may be explained by the instability of lake ecology due to the fluctuation of the salinity and acidity of the water. An additional aim was to assess if dung fungi in lacustrine sediments reflect changes in human population density around the lake. We found that neither historical sources of human presence nor the influx of coprophilous fungi are correlated with the inferred climate changes. Coprophilous fungi can be used as individual or additional sources of assessment for the peopling and human-related herbivore density including overgrazing of the studied area.