The detailed facies and physical stratigraphic analysis of the Primary Lower Gypsum in the Mediterranean indicates a surprising bed-by-bed correlation at basin-scale (Spain, Italy, Hellenic arc and Cyprus arc), that is tuned to the orbital calibration for the first stage of the Messinian salinity crisis from 5.96 to 5.61 Ma ago. A total of 16, precessionally-controlled, gypsum cycles were deposited rapidly in less than 350 ka, forming sequences up to 300 m thick. The lack of subaerial exposure features and the common facies associations and stacking pattern for sections located thousands of kilometers apart in different geological settings indicates a modest depositional depth, not extremely shallow. Selenite deposition occurred only at the bottom of restricted marginal basins less than 200 m deep, while no gypsum could precipitate in the deeper euxinic Mediterranean portions where only thin and barren shale/dolostone couplets formed. The lowermost selenite beds pass laterally to dolomite-rich limestones interbedded with barren euxinic shales in poorly oxygenated settings, indicating that the gypsum sedimentation was diachronous and did not necessarily mark the onset on the Messinian salinity crisis. Evaporite facies sequences (EF1 to 8) within individual gypsum beds show small-scale, subaqueous sedimentary cycles that mimic regressive–transgressive cycles: a) initial evaporite precipitation at relatively low supersaturation produced the massive selenite (facies EF3) in a relatively deep setting; b) continuous evaporation and drawdown by oscillating brine level formed the banded selenite (EF4) at the aridity acme of the precessionally-controlled cycle; c) general progressive brine level rise with strong brine flow led to the formation of large selenite supercones branching laterally (supercones in Spain and branching selenite, EF5, in the rest of the Mediterranean); and d) flooding by undersaturated continental water terminated gypsum precipitation with the deposition of argillaceous sediments (EF1, Northern Apennines), and/or limestone (EF2, Sicily and Spain) during the humid phase in the precession climate cycle. The stacking pattern and selenite facies associations suggest an overall shallowing-upward trend with a basin-wide hydrologic change starting from the 6th cycle (5.84 Ma), which is marked by the appearance of the branching selenite facies (supercones) in Spain and indicates that the brines became current-dominated. The Sr-isotope stratigraphy suggests that in the Northern Apennines the brines were strongly modified by continental waters ( 87 Sr/ 86 Sr = 0.708893 to 0.708998), and received direct pulses of Atlantic seawater ( 87 Sr/ 86 Sr = 0.70900 to 0.709024) only in the upper part of the section. In areas away from the mainland, such as Sicily, the continental input was by far less important.