The lakes of Chalain and Clairvaux (Jura, France) preserve, in the wet sediments of their low marshes and lakeshores, the remains of palafittes dating from the Neolithic and Bronze Age. These sites have been intensively studied since the 1970s, but the environment around the lakes where these populations lived remains a field that remains to be explored. With this in mind, a team of researchers has embarked on a new research project, formulating the problem of the exploitation of the surrounding area of Lake Chalain. A multi-disciplinary research programme is underway on the shores of the two Jura lakes: “Agriculture and livestock farming around the Jura lakes since the Neolithic: the contribution of palaeo-environmental and archaeo-pedological data”. Electromagnetic frequency prospecting provides an effective protocol for searching for signals linked to traces of ancient agricultural practices. Once the points of interest had been identified, archaeo-pedological surveys were carried out and a battery of analyses was used to study the samples. Geophysical prospecting revealed a spatial distribution of hearths, and boreholes were opened on these anomalies. Analyses revealed two main horizons that were identified as vestiges of agricultural practices, one dated to the medieval period (890– 1020 cal AD) and consisting of the remains of agricultural hearths; the other, older (2900–2680 cal BC and 3350–3100 cal BC), took the form of a thin black layer with charcoal and burnt clay granules. These pedo-archaeological observations indicate that these environments have undergone irreversible pedological changes since Neolithic farming began. Contrary to previous schemes, which defined agriculture developed over large areas, the recent hypothesis illustrated by these results rather envisages agriculture restricted to peri-lacustrine zones subject directly to fluctuations in lake levels. This hypothesis would help to explain the absence of Neolithic sites during periods of high lake levels, when the climate was cooler and wetter. Given the high archaeological potential of these sites in terms of the relationship between societies and environments, this multidisciplinary programme will provide a stimulus for innovative research on these major sites and offer an opportunity to gain a better understanding of the way of life of the inhabitants of the Jura pile dwellings.