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This research first focuses on the spatial and temporal patterns of heavy metals from contrasting environments (highly polluted to deepwater sites) of Lake Geneva. The mercury (Hg) and lead (Pb) records from two deepwater sites show that the heavy metal variations before the industrial period are primarily linked to natural weathering input of trace elements. By opposition, the discharge of industrial treated wastewaters into Vidy Bay of Lake Geneva during the second part of the 20th century, involved the sedimentation of highly metal-contaminated sediments in the area surrounding the WWTP outlet pipe discharge. Eventually, a new Pb isotope record of sediments from Lake Lucerne identifies the long-term increasing anthropogenic lead pollution after ca. 1500, probably due to the development of metallurgical activities during the High Middle Ages. These data furthermore allows to compare the recent anthropogenic sources of water pollution from three of the largest freshwater lakes of Western Europe (lakes Geneva, Lucerne, and Constance). High increases in Pb and Hg highlight the regional impact of industrial pollution after ca. 1750-1850, and the decrease of metal pollution in the 1980s due to the effects of remediation strategies such as the implementation of wastewater treatment plants (WWTPs). However, at all the studied sites, the recent metal concentrations remain higher than pre-industrial levels. Moreover, the local scale pollution data reveal two highly contaminated sites (N 100 μg Pb/g dry weight sediment) by industrial activities, during the late-19th and early-20th centuries (Lake Lucerne) and during the second part of the 20th century (Vidy Bay of Lake Geneva). Overall, the regional scale pollution history inferred from the three large and deep perialpine lakes points out at the pollution of water systems by heavy metals during the last two centuries due to the discharge of industrial effluents.