In central Western Europe, several studies have shown that colder Holocene periods, such as the Little Ice Age, also correspond to wet periods. However, in mountain areas which are highly sensitive to erosion processes and where precipitation events can be localized, past evolution of hydrological activity might be more complicated. To assess these past hydrological changes, a paleolimnological approach was applied on a 13.4-m-long sediment core taken in alpine Lake Anterne (2063 m asl) and representing the last 3.5 ka. Lake sedimentation is mainly composed of flood deposits triggered by precipitation events. Sedimentological and geochemical analyses show that floods were more frequent during cold periods while high-intensity flood events occurred preferentially during warmer periods. In mild temperature conditions, both flood patterns are present. This underlines the complex relationship between flood hazards and climatic change in mountain areas. During the warmer and/or dryer times of the end of Iron Age and the Roman Period, both the frequency and intensity of floods increased. This is interpreted as an effect of human-induced clearing for grazing activities and reveals that anthropogenic interferences must be taken into account when reconstructing climatic signals from natural archives.