During the first stage of the Late Miocene Messinian salinity crisis (5.97–5.60 Ma), deposition of sulfates (the Primary Lower Gypsum) occurred in shallow silled peripheral subbasins of the Mediterranean undergoing restricted water exchange with the Atlantic Ocean. Fluid inclusions in Messinian selenite crystals from the Piedmont Basin (northwest Italy) have surprisingly low salinities (average of 1.6 wt% NaCl equivalent), suggesting that parent waters were depleted in Na+ and Cl– compared to modern seawater. Modern gypsum from a Mediterranean salt work, in contrast, contains fluid inclusions with elevated salinities that match the normal evaporation trend expected for seawater. The salinity data indicate that the Messinian sulfate deposits from the Piedmont Basin formed from hybrid parent waters: seawater mixed with Ca2+ and SO42– enriched freshwaters that dissolved coeval marginal marine gypsum. Such mixed parent waters and complex recycling processes should be taken into account when explaining the genesis of other Messinian gypsum deposits across the Mediterranean Basin.