Like other lakes in France and Europe, French Jura lakes are currently the subject of fierce controversy following a large number of research studies carried out in a variety of disciplines. The presence of abnormal quantities of certain trace metals has created a climate of apprehension among lake users and caused administrators sit up and take notice. As water reservoirs for medium-and high-altitude mountain towns and villages as well as leisure and recreation areas for large numbers of tourists, the lakes are highly-valued heritage sites. They also generate considerable income for local authorities and to a certain extent for the state. Long-term hydrological monitoring and analysis of the sediments of nine lakes in the Franche-Comte region of eastern France has enabled the physical-chemical processes regulating their functions over the last 300 years to be understood and questions concerning the origin and extent of the lakes' pollution to be answered. The analyses confirmed that the lakes ' water is of local origin, from within their respective catchment areas, and that it stays in the lakes for between 10 and 12 months. Isotopic analyses showed that surface water is young (H3 around -10 UT), while a graph of H2 as a function of O18 gave a surface precipitation altitude corresponding to the mean altitude of each lake's catchment area. The relatively high rates of heavy metals, mainly Pb, V, Zn, Cu, Ni, Co and Cr, originated from outside the basin. The isotopic ratios of Pb (204Pb, 206Pb, 207Pb and 208Pb) allowed three sources of deposits to be identified: the first is lithogenic at deep lake levels and corresponds to the composition of the continental crust; human for upper levels at depths of 0-17 cm, mainly due to industrial discharges (leaded petrol, the coal industry, steelworks, etc.); while an intermediate origin mingles both these sources. Metals are first recorded from the 1880s, the era of the Industrial Revolution. These trace metal deposits peaked in the 1960s and 1970s and have mostly begun declining. Enrichment factors were calculated by using three lithogenic elements (Th, Zr, La) and by taking the core sample from Lake Saint-Point as a base sample. This confirmed the human origin and rate of succeeding deposits since the middle of the Industrial Revolution. There are frequent exchanges between metal and water, and recent increases in the content of certain elements have caused concern. The aim of this study was to understand the exchanges taking place at the deepest levels of the water column following changes in the physical-chemical conditions of the lakes ' environment.