During Messinian time, the Mediterranean underwent hydrological modifications culminating 5.97 Ma ago with the Messinian salinity crisis (MSC). Evaporite deposition and alleged annihilation of most marine eukaryotes were taken as evidence of the establishment of basin-wide hypersalinity followed by desiccation. However, the palaeoenvironmental conditions during the MSC are still a matter of debate, chiefly because most of its sedimentary record is buried below the abyssal plains of the present-day Mediterranean Sea. To shed light on environmental change at the advent and during the early phase of the MSC, we investigated the Govone section from the Piedmont Basin (NW Italy) using a multidisciplinary approach (organic geochemical, petrographic, and carbon and oxygen stable isotope analyses). The Govone section archives the onset of the crisis in a succession of organic-rich shales and dolomite-rich marls. The MSC part of the succession represents the deep-water equivalent of sulphate evaporites deposited at the basin margins during the first phase of the crisis. Our study reveals that the onset of the MSC was marked by the intensification of water-column stratification, rather than the establishment of widespread hypersaline conditions. A chemocline divided the water column into an oxygen-depleted, denser and more saline bottom layer and an oxygenated, upper seawater layer influenced by freshwater inflow. Vertical oscillations of the chemocline controlled the stratigraphic architecture of the sediments pertaining to the first stage of the MSC. Accordingly, temporal and spatial changes of water masses with different redox chemistries must be considered when interpreting the MSC event.