Gypsum makes up about one fifth of giant salt deposits formed by evaporation of seawater throughout Earth’s history. Although thermodynamic calculations and precipitation experiments predict that gypsum precipitates when the salinity of evaporating seawater attains about 110 g kg-1, gypsum deposits of the Mediterranean Salt Giant often bear the geochemical signature of precipitation from less saline water masses. Addressing this geochemical riddle is important because marine gypsum deposition and continental gypsum erosion affect the global carbon cycle. We investigated gypsum deposits formed in the marginal basins of the Mediterranean Sea during the Messinian Salinity Crisis (about 6 million years ago). These often bear low-salinity fluid inclusions and isotopically light crystallization water, confirming previous published reports that the Mediterranean Salt Giant harbors low-salinity gypsum deposits. A geochemical model constrained by fluid inclusion salinity and isotope (87Sr/86Sr, d34SSO4, d18OH2O, dDH2O) measurements excludes that Ca2+- and SO42--enriched continental runoff alone provides the trigger for gypsum precipitation at low salinity. We propose that, concurrent with the prevalent evaporative conditions and with Ca2+- and SO42--bearing runoff, the biogeochemical sulfur cycle is capable of producing a spatially-restricted and temporally- transient increase of Ca2+ and SO42- within benthic microbial mats, creating local chemical conditions conductive to gypsum precipitation. This hypothesis is supported by the presence of dense packages of fossils of colorless sulfur bacteria within gypsum in several Mediterranean marginal basins, together with independent geochemical and petrographic evidence for an active biogeochemical sulfur cycle in the same basins. Should this scenario be confirmed, it would expand the range of environments that promote marine gypsum deposition; it would also imply that an additional, biological coupling between the calcium, sulfur and carbon cycles exists.