Oxygenation of Earth's oceans and atmosphere through time has consequences for subducted surface signatures that are now stored in the mantle. Here, we report significant mass-dependent selenium isotope variations in modern hot spot-influenced oceanic lavas. These variations are correlated with tracers of mantle source enrichment, which can only be explained by incorporation of abyssal pelagic sediments subducted from a redox-stratified mid-Proterozoic ocean. Selenium geochemical signatures of these sediments have mostly been preserved during long-term recycling and may therefore complement the global surface sediment record as ancient oxygen archives. Combined deep mantle and surface perspectives, together with emerging models for atmospheric oxygen based on selenium systematics, further imply a significantly oxygenated ocean-atmosphere system throughout the mid-Proterozoic.