Eukaryotic life expanded during the Proterozoic eon¹, 2.5 to 0.542 billion years ago, against a background of fluctuating ocean chemistry^2-4. After about 1.8 billion years ago, the global ocean is thought to have been characterized by oxygenated surface waters, with anoxic and sulphidic waters in middle depths along productive continental margins and anoxic and iron-containing (ferruginous) deeper waters^5-7. The spatial extent of sulphidic waters probably varied through time^5,6, but this surface-to-deep redox structure is suggested to have persisted until the first Neoproterozoic glaciation about 717 million years ago^8-11. Here we report an analysis of ocean redox conditions throughout the Proterozoic using new and existing iron speciation and sulphur isotope data from multiple cores and outcrops. We find a global transition from sulphidic to ferruginous mid-depth waters in the earliest Neoproterozoic, coincident with the amalgamation of the supercontinent Rodinia at low latitudes. We suggest that ferruginous conditions were initiated by an increase in the oceanic influx of highly reactive iron relative to sulphate, driven by a change in weathering regime and the uptake of sulphate by extensive continental evaporites on Rodinia. We proposethat this transition essentially detoxified oceanmargin settings, allowing for expanded opportunities for eukaryote diversification followingaprolonged evolutionary stasis before one billion years ago.