The road to the Messinian salinity crisis was paved with increasing environmental stress in the Mediterranean marine realm. The nature and origin of the crisis of the marine biota is still matter of debate because the crisis itself hinders univocal paleoenvironmental reconstructions by selecting the most resilient taxa, which are generally adapted to a wide range of stresses. The commonly accepted hypothesis, recently reiterated, is that increasing salinity was the main factor eliminating the marine biota from the geological record and eventually leading to the deposition of evaporitic carbonates in the Eastern Mediterranean just before the onset of the crisis dated at 5.97 Ma. We suggest that stratification and increasing restriction (continental water influence), leading to strong variability of surface water conditions, better explain the 87Sr/86Sr excursion below the global ocean value and the pattern of calcareous plankton events in the uppermost portion of the Metochia section (Gavdos Island, Greece), from 6.24 to 5.95 Ma. The early reduction of foraminifera at 6.07 Ma, typical of relatively deep successions lacking primary gypsum during the first phase of the crisis, precedes a sequence of calcareous nannofossil events such as the influx of Braarudosphaera bigelowi at 6.168 Ma, the acme of Reticulofenestra perplexa at 6.058–6.018 Ma, and the peaks of Sphenolitus spp. and Helicosphaera carteri at 5.99 and 5.973 Ma, respectively. The peak of such opportunistic calcareous nannofossil and the foraminifer disappearance, commonly observed in both deep and shelf successions, closely approximate the onset of the Messinian salinity crisis, regardless the occurrence of the Primary Lower Gypsum unit, and is interpreted as the final restriction step, which led to a 600 ky environmental perturbation culminating with the deposition of the Mediterranean salt giant.