Forest vegetation plays a key role in the cycling of mercury (Hg) and organic matter (OM) in terrestrial ecosystems. Litterfall has been indicated as the major transport vector of atmospheric Hg to forest soils, which is eventually transported and stored in the sediments of forest lakes. Hence, it is important to understand how changes in forest vegetation affect Hg in soil and its biogeochemical cycling in lake systems. We investigated the pollen records and the geochemical compositions of sediments from two lakes (Schurmsee and Glaswaldsee) in the Black Forest (Germany) to evaluate whether long-term shifts in forest vegetation induced by climate or land use influenced Hg accumulation in the lakes. We were particularly interested to determine whether coniferous forests were associated with a larger export of Hg to aquatic systems than deciduous forests. Principal components analysis followed by principal component regression enabled us to describe the evolution of the weight of the latent processes determining the accumulation of Hg over time. Our results emphasize that the in-lake uptake of Hg during warm climate periods, soil erosion after deforestation and emissions from mining and other human activities triggered changes in Hg accumulation during the Holocene stronger than the changes caused by forest vegetation alone.