Description: Land cover transformations have accompanied the rise and fall of civilizations for thousands of years, exerting strong influence on the surrounding environment. Soil erosion and the associated outwash of nutrients are a main cause of eutrophication of aquatic ecosystems. Despite the great challenges of water protection in the face of climate change, large uncertainties remain concerning the timescales for recovery of aquatic ecosystems impacted by hypoxia. This study seeks to address this issue by investigating the sedimentary record of Lake Murten (Switzerland), which witnessed several phases of intensive human land-use over the past 2000 years. Application of geophysical and geochemical methods to a 10 m-long sediment core revealed that soil erosion increased drastically with the rise of the Roman City of Aventicum (30 CE). During this period, the radiocarbon age of the bulk sedimentary organic carbon (OC) increasingly deviated from the modeled deposition age, indicating rapid flushing of old soil OC from the surrounding catchment driven by intensive land-use. Enhanced nutrient delivery resulted in an episode of cultural eutrophication, as shown by the deposition of varved sediments. Human activity drastically decreased towards the end of the Roman period (3rd century CE), resulting in land abandonment and renaturation. Recovery of the lake ecosystem from bottom-water hypoxia after the peak in human activity took around 50 years, while approximately 300 years passed until sediment accumulation reached steady state conditions on the surrounding landscape. These findings suggest that the legacy of anthropogenic perturbation to watersheds may persist for centuries.