The formation and dissolution of salt giants impacts ocean chemistry on thousand-million year timescales. Gypsum precipitation and weathering changes the oceanic calcium concentration with implications for the carbon cycle and global temperatures. However, the connectivity of salt giants with the global ocean is necessarily restricted, making the timing of Ca2+ extraction and return more uncertain. Here we reconstruct the final phase of gypsum precipitation of the Late Miocene Mediterranean Salt Giant using micropaleontology, sedimentology and 87Sr/86Sr analyses on the most complete record preserved at Eraclea Minoa on Sicily and explore its implications for global climate. Precessional gypsum-marl couplets (Upper Gypsum) characterize the last 200 kyrs (Stage 3) of the Messinian Salinity Crisis (MSC; 5.97–5.332 Ma) in both intermediate (500–1000 m) and deep (>1000 m) Mediterranean basins. The interbedded selenitic gypsum layers contain well-preserved calcareous nannofossil assemblages dominated by Reticulofenestra minuta, a marine species which tolerates stressful conditions. Marine water is also required to explain the gypsum 87Sr/86Sr data, which describe a small range of ratios (0.708704–0.708813) lower than coeval ocean water. Mass-balance calculations indicate that during gypsum precipitation, the Atlantic made up ≤20% of a Mediterranean (“Lago-Mare”) water mass dominated by low salinity discharge from large river systems and Eastern Paratethys. This suggests episodic extraction of calcium and sulfate ions from the ocean throughout MSC Stage 3. The marls commonly contain shallow (30–100 m) brackish-water ostracods of Paratethyan (Black Sea) origin. Marls with Paratethyan ostracods are also found in both marginal (<500 m) and deep Mediterranean settings. This indicates that marl-deposition was not synchronous across the basin, but that it occurred in intermediate and deep basins during base-level lowstands at insolation minima and on the shallow Mediterranean margins during insolation maxima-driven highstands. These high-amplitude base-level fluctuations exposed the evaporites to weathering, but ponded the products in the Mediterranean basin until reconnection occurred at the beginning of the Pliocene.