Callovian–Oxfordian calcareous nannofossils are documented from four sections distributed along a proximal–distal (slope to central basin) transect in the French Subalpine Basin (south-eastern France). The sections were dated and correlated using integrated ammonite, dinoflagellate and nannofossil biostratigraphies. The nannofossil assemblages are constantly dominated by Watznaueria britannica. However, significant spatial changes in nannofossil assemblage composition are recorded. Nannofossil assemblages recovered in slope and slope-to-basin transition sections are characterized by high abundances, lowest diversities, highest percentages of smallest-sized morphotypes of W. britannica, subordinated W. britannica/manivitiae (a morphotype described in this study), and are indicative of turbulent, unstable and/or eutrophic conditions. Towards the central part of the basin, as the nutrient content and turbulence declined and paleoenvironmental stability increased, the nannofossil assemblages become more diverse and characterized by lower relative abundances of W. britannica but higher contribution of larger morphotypes and higher relative abundances of W. barnesiae/fossacincta, Biscutum dubium and Zeugrhabdotus erectus. These latter small coccoliths, markers of high surface-waters fertility for the Cretaceous, were probably not competitive with respect to smaller-sized W. britannica in unstable and eutrophic surface waters for the Jurassic. An increase in the surface water productivity is recorded both in proximal and distal sections at the Callovian–Oxfordian transition, and is demonstrated both by an increase in nannofossil total abundances and in the relative abundances of taxa adapted to high-trophic levels. Thermal minimum in surface waters, as indicated by an increase in the percentages of the cool-water nannofossil taxa, is associated to increased productivity. Further studies will be necessary to demonstrate whether surface-water productivity changes, already recorded in the eastern Paris Basin, were global.