The Joux Valley (Swiss Jura Mountains) has a rather unusual history of human occupation, characterized by tardive but extensive settlement since the Late Middle Ages, followed by an intensive period of industrial development. To estimate the links between human activities and environmental consequences, sediment cores were retrieved in Lake Joux and submitted to a multiproxy analysis (high-resolution photographs, magnetic susceptibility, density, x-ray fluorescence, grain size, organic geochemistry, ¹⁴C, ²¹⁰Pb and ¹³⁷Cs dating). The diversity of anthropication phases, defined from historical data, is clearly recognized in the lake archive. The record suggests the region was mainly under climatic influence until the end of the 13th century. The growth of settlements in the valley and the associated massive deforestation is recorded by increasing terrestrial inputs, reflecting large-scale soil destabilization, which subsequently persists despite the transition from farming to industrial activities. Autochthonous contributions then dominate the record, both in response to climatic and anthropogenic influences. Construction works conducted at the outlet of the lake affected water flow, sedimentation and aquatic community (macrophytes, ostracods) dynamics. The substantial increase of anthropogenic heavy metals (Fe, Zn, Pb) recorded during the 20th century could reflect the development of the watch-making industry in the area, as well as the use of leaded gasoline. Historical information facilitated interpretation of the observed paleolimnological evolution in the context of varied coexisting human activities. This study highlights the importance of applying an integrated paleolimnological-historical approach in order to establish clear links between well-defined human activities and their subsequent environmental responses through time.