The Lower Freshwater Molasse of western Switzerland comprises a thick series of continental deposits of Late Oligocene-Early Miocene age. Fresh-water carbonates occur at two main horizons within this succession. Lower Chattian “palustrine” carbonates (Calcaires Inférieurs) show a shallow fresh-water fauna/flora of ostracods and charophytes, but display clear evidence of subaerial exposure in the form of glaebule/pisoid formation, circumgranular cracking, rhizoliths and microkarstic cavities. Repeated desiccation led to locally intense modification by pedogenesis. These horizons record the development of shallow, ephemeral lakes at the northern margin of the Swiss Molasse Basin. Stable isotope analyses were carried out on 46 calcite samples. Data from matrix and intraclasts reveal typical fresh-water compositions ( δ 13C = −5 to −7.5‰; δ 18O = −5.5 to −9‰). A weak co-variant trend suggests deposition in hydrologically closed lakes, although the range of δ 13C values recorded is also consistent with pedogenetic overprinting associated with subaerial exposure. Spar cements and vadose crystal silts display δ 13C compositions from −6 to −7‰, but show light δ 18O values (from −10 to −11‰), recording formation from meteoric waters. Upper Chattian carbonates (Calcaires d'eau douce et dolomie) include algal-ostracodal laminites, interpreted as profundal lake deposits, as well as bioturbated shallow lake charophyte-ostracod mudstones and wackestones, sandy wackestones and white dolomite. Stable isotope analyses (20 calcites, 2 dolomites) show δ 13C values from −2 to −6‰, and δ 18O from −6 to -11‰. Data for laminites and biomicrites plot in different fields; variations in carbon isotopic composition may be attributable to higher organic productivity during high lake stands (the laminites show heavier δ 13C values) or to areal differences in the proportions of biogenic, authigenic and detrital carbonate ( δ 13C values are generally higher in areas of greater detrital carbonate supply). The heavier δ 18O values shown by the dolomites ( δ 13 C = −3‰ = δ 18 O = 0 to −1‰) suggest formation from evolved, evaporitic lake waters. These carbonates record deposition in an extensive, possibly deeper lake complex subject to clastic input from the Alps in the south.