Cyanobacterial blooms in water bodies have occurred on a worldwide basis in the last few decades, and knowledge of their occurrence under natural conditions, and of the mechanisms responsible, is important for understanding their origin. However, little is known about the long-term trends in cyanobacterial abundance in the pre-industrial era, and its causes. Traditional microscope analysis of microfossil plankton is widely applied in paleoecology, yet the majority of phytoplankton (e.g., cyanobacteria) are not preserved as microfossils in sediments, although they can leave a fingerprint in the form of sedimentary ancient DNA (sedaDNA). Here, sedaDNA is used for the first time to reconstruct the history of phytoplankton communities in a crater lake in northern China over the past two millennia. Our data show that changes in phytoplankton community structure and diversity were linked to temperature and precipitation variations during ∼0–1400 Common Era (CE). However, after ∼1400 CE the cyanobacterial abundance increased to an unprecedented degree, and cyanobacteria (mainly composed of Synechococcus) became disproportionately dominant relative to other phytoplankton. This rise was concomitant with increased aeolian dust input by winds driven by an intensified Siberian High, which resulted in increased dust transport across the entire mid-latitude region of the Northern Hemisphere. This suggests that dust input can exceed natural climatic variability as the dominant control on lake ecosystems in regions subject to dust deposition. We suggest that future lake ecological management strategies in areas of dust deposition should consider not only the influence of climatic warming but also the impact of nutrient inputs delivered by dust storms.