The Pliocene ria, a narrow seaway running up the Rhône Valley, has been mapped for a while by field geologists. Only much later, after the DSDP Leg 13 in 1970, a consensus was reached that this unique geological feature of the Rhône Valley was created by the major Mediterranean sea-level drop associated with the Messinian Salinity Crisis, followed by a sudden sea-level rise caused by the breach of the Strait of Gibraltar and the invasion of the Mediterranean Basin by the Atlantic waters. At the regional level of the Lyon Metropolis in the upper Rhône Valley, main issues were however remaining about the course and depth of the Messinian valley, and about the valley fill, namely where and how do the Pliocene marine strata of the Rhône Valley pass to the continental deposits of the Bresse Basin to the north? These are key-questions in that the Plio-Pleistocene makes up a large fraction of the basement that holds up a large city, not free from potential geological hazards and subject to problems of groundwater management, high-cost tunneling projects, etc. Our survey reviews first the historical researches À descriptions of the outcrops and fossil assemblages. It is followed by an unprecedented analysis and correlation of a thousand boreholes, which makes it possible to physically link and reconcile ancient local observations. Sections across the Messinian valley reveal a proper canyon morphology for the segments that cut the crystalline basement. The magnitude of the incision has been calculated as 335 m to a minimum, three hundred kilometers away from the river mouth. Three major depositional systems are distinguished for the Pliocene À Lower Pleistocene succession. The valley that initially ran much farther north of Lyon was occupied in the Zanclean by a series of pounded lakes, dammed by transverse local alluvial fans, filled by minor Gilbert-type deltas, and repeatedly flooded by marine ingressions. The valley wings were then encroached during the Piacenzian by a major, Alps-rooted alluvial sheet. At the level of Lyon, the fluvial deposits were deflected to the north (Sables de Trévoux) and to the south (Alluvions jaunes) as a dichotomy. The succession was then capped by a gravel-dominated fluvio-glacial fan (Alluvions jaunes sommitales) at the Plio-Pleistocene transition. It spread out from the north-east to the south, and intersected the previous valley overfill due to the shift to the north, i.e., South Jura, of the feeder stream. The depositional and current elevations of the marine-influenced episodes, i.e. marker bands that punctuate the regional Neogene succession, are used to bring out successive uplift and subsidence phases of the region. Finally, we tentatively link the major shifts in the depositional patterns of the Late Neogene succession in the Lyon area to major changes in the thrust belt activity, exhumation story, and outset of glaciers in the western Alps.