Although humans have impacted their environment over millennia, details of these impacts, especially on aquatic systems, is still surprisingly scarce despite potential disturbance by early land use. This study examined a high-resolution radiocarbon-dated Holocene record from the Danish Lake Væng, using geochemical and biological proxies, and related the observed impacts to other lake records with catchment disturbance. The results indicate a lengthy and varying history of aquatic eutrophication linked to human activity. Modest impacts on the lake coincided with the first signs of landscape disturbance during the Neolithic (c. 4500 cal. yrs BP). Observed impacts intensified in the Late Bronze and Pre-Roman Iron Age. Viking Age/Medieval deforestation and erosional inputs to the lake associated with new ploughing technology (1200 cal. yrs BP), however, led to a major reorganisation of the aquatic ecosystem. Filamentous bloom-forming cyanobacteria, common today in heavily culturally impacted lakes, reached a historical maxima. The lake ecosystem subsequently recovered somewhat but remains eutrophic to date. The erosion record from Lake Væng shows a striking similarity with other Danish lake records, especially the notable increase in Medieval Period catchment inputs, which are observed in other European lacustrine records. Numerous European lowland lakes may have shifted into a degraded ecological state millennia ago, but degradation intensified during the onset of the Medieval Period. Hence, assuming pre-industrial conditions as relatively pristine reference baselines for more recent cultural eutrophication could be flawed in landscapes intensively used by humans for millennia.