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The reconstruction of human-driven ecosystem dynamics under the background of climate change is crucial for understanding past human-environment interactions and gaining insights into the evolution of aquatic ecosystems that are currently facing eutrophication. However, disentangling the effects of human activities from climate warming on lake ecosystem presents challenge due to limited knowledge of spatial and temporal response mechanisms of ecosystem evolution from climate-driven processes to those influenced by both climate and mild human intervention, and ultimately to those primarily driven by intense human activities. Here, we use diatom analysis of a sediment core from Dianchi Lake on the southeastern margin of the Tibetan Plateau to reconstruct environmental changes, with particular emphasis on the influences of climate, changing vegetation, and land-use on lake ecosystems. By comparing fossil diatom assemblages with previous reconstructions of vegetation and catchment processes, we demonstrate three successive stages of nutrient enrichment in Dianchi Lake over the past 20,000 years. The first major transition, occurring at the late glacial/Holocene boundary, witnessed an increase in nutrient inputs primarily driven by Holocene climate warming. The most pronounced nutrient enrichment, characterized by significant changes in diatom assemblages around 2.3 cal kyr BP, resulted from intensified agricultural cultivation. The arrival of the Han people to the Dianchi lake basin has been followed by extensive burning, land clearance, and increased soil erosion associated with agricultural production, marking the early detectable human impact on aquatic ecosystems since 2.3 cal kyr BP. Despite the eutrophication observed in Dianchi Lake in the last century, the long-term diatom record indicates that the lake ecosystem experienced abrupt state transformations as early as 2.3 cal kyr BP. The decline in water level due to dredging for flood control, coupled with intensified soil erosion and exposure of alluvial deposits during the period of 750–250 cal yr BP, triggered exceptionally low lake productivity and vegetation changes, indicating a collapse of the lake ecosystem due to intensified human impacts. This underscores the limnological effects of transitioning from predominantly agricultural practices to large-scale hydrological modifications for irrigation and agricultural development. The accelerated soil erosion and rapid water level decline since 2.3 cal kyr BP represent a tipping point for both the lake ecosystem and catchment vegetation, with significant implications for present-day land and lake degradation. To prevent further degradation of the lake and mitigate the impacts of climate warming, we propose: (1) enhancing lake ecosystem management through the promotion of diverse forests and crops within the landscape, and (2) fostering diverse cultural relationships between people and their water and land resources. Our study provides evidence that the impact of local anthropogenic activities on aquatic ecosystem functions and services can outweigh that of climate change, particularly since the onset of significant human influence. • Diatom analysis reconstructs 20,000-year environmental history of Dianchi Lake, disentangling human and climate impacts. • Intensified agriculture around 2.3 cal kyr BP caused significant nutrient enrichment and detectable human impact on Dianchi Lake's aquatic ecosystems. • Accelerated soil erosion and water level decline since 2.3 cal. kyr BP mark a tipping point for the lake ecosystem. [ABSTRACT FROM AUTHOR]