© 2019 Elsevier B.V. New sedimentological, micropaleontological and geochemical data from the Upper Miocene pre-evaporitic sedimentary sequence of the Faneromeni section (Crete Island, eastern Mediterranean) revealed a stepwise restriction of the Mediterranean Sea preceding the Messinian Salinity Crisis (MSC), which was modulated by a sedimentary cyclicity responding to orbital parameters. This cyclicity is manifested by lithological alternations from laminated to indurated homogeneous marls and clayey limestones, and covers the Tortonian-Messinian Transition (TMT; 7.6–6.7 Ma). This time window covers the successive closure of the marine Mediterranean-Atlantic gateways, which culminated in the onset of the MSC. In the present study, we present the first evidence for changes in the upper water column reflected by sea surface temperature (SST) and salinity (SSS) variations that correlate with pronounced paleoclimatic fluctuations. Planktonic foraminiferal isotopes, in combination with paired mixed layer Sr/Ca-derived SST data, reveal that the very warm late Tortonian interval has been followed by a strong long-term cooling (~10 °C) and desalination (~10‰) trend during the earliest Messinian, attributed to the paroxysmal phase of the so-called “siphon” event. In particular, the climate shift that occurred at the end of a global carbon isotope (δ13C) decrease suggests that changes in the carbon cycle were instrumental in driving late Miocene climate dynamics (cooling and aridity) in the progressively isolated eastern Mediterranean Sea. The observed salinity variability during this time interval also provides further insights about seasonal freshwater inputs and gives new support to the much-debated hydrologic regime (linear salinity increase vs step-function evolution with strong salinity fluctuations) preceding the deposition of evaporites. The novel methodology of foraminiferal Sr/Ca paleothermometry and results of this study could have numerous potential applications to other regions and relevant extreme geological events. Therefore, in the near future we expect this approach to add important new information to our understanding of Neogene climates.