This study used organic matter in oligotrophic Lake Constance (southern Germany) to reconstruct lake environment and to disentangle the multiple factors, such as climate change and human impacts, which influence sedimentation in large lakes. A sediment core from Upper Lake Constance, which represents 16,000 years of Late Glacial and Holocene lake history, was analysed for organic biomarkers, hydrogen index and elements calcium, strontium, and magnesium. Magnetic susceptibility was measured to establish a high-resolution stratigraphic framework for the core and to obtain further information about changes with respect to relative allochthonous versus autochthonous sedimentation. Dinosterol-a biomarker for dinoflagellates-and calcium have low concentrations in Younger Dryas sediments and consistently high concentrations between 10,500 and 7,000 cal. years BP. These variations are attributed to changes in lake productivity, but are not reflected in the proportion of total organic carbon within the sediment. During the Younger Dryas and between 6,000 and 2,800 cal. years BP, concentrations and accumulation rates of land-plant-derived C29-steroids (β-sitosterol, stigmastanol and stigmasterol), in combination with a relatively low HI, indicate periods of enhanced terrigenous input to the lake. For the Younger Dryas, higher runoff can be attributed to a cold climate, leading to decreased vegetation cover and increased erosion. After 6,000 cal. years BP, high terrestrial input may be explained by enhanced precipitation. Biomarker and HI results, in combination with archaeological studies, raise the question as to whether lakeshore settlements affected sedimentation in Upper Lake Constance between 6,000 and 2,800 cal. years BP. © 2008 Springer Science+Business Media B.V.