The Gulf of Corinth is a rapidly rifting basin that has been alternately connected to/isolated from the Mediterranean due to Quaternary global sea levels fluctuations. A recently retrieved sediment record from the Gulf of Corinth (IODP Expedition 381) shows variations in magnetic susceptibility, with relatively higher and more variable values in isolated/glacial sediments and lower, more stable values in connected/interglacial sediments. Using geochemical methods, we find that not the primary input of magnetic minerals, but diagenetic processes generated the magnetic susceptibility pattern. Easily reducible sulphides (most likely greigite) increase in high magnetic susceptibility (isolated/glacial) sediments, whilst magnetite shows no systematic relationship to magnetic susceptibility. After discounting several possible causes for the formation and preservation of greigite (bottom water redox conditions, high sedimentation rates, reactive Fe and organic matter availability), a decrease in sulphate concentrations in the Gulf of Corinth during isolated/glacial periods is the most likely explanation, supporting parallel microfossil evidence for a freshening of the water column. This sulphate limitation appears to stall sedimentary pyrite formation at the stage of ferrimagnetic monosulphides like greigite. Greigite formation as an indicator of paleosalinity variations has been observed in other depositional settings (e.g., Chesapeake Bay, the Baltic Sea, the Miocene Paratethys and the Black Sea), supporting our interpretation. Specific to the Gulf of Corinth, linking a proxy for basin connectivity to a high resolution (at least 40, and up to 7 year temporal resolution) magnetic susceptibility record over 750,000 years offers an opportunity to investigate, in detail, the tectonic evolution of this rift basin and its link to global sea level fluctuations.