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Earth’s core-mantle segregation set the initial conditions for its subsequent evolution. However, the effect of water on core-mantle element partitioning remains poorly constrained. Using machine learning molecular dynamics simulations trained on quantum mechanical data, we show that increasing water content promotes magnesium partitioning into the metallic core, whereas silicon, iron, and hydrogen increasingly prefer the silicate mantle. On the basis of Earth’s core mass fraction and oxygen fugacity during core formation, a self-consistent hydrous core-mantle differentiation model yields a bulk Earth water content of ~0.23 weight % (equivalently ~10 ocean masses), a bulk Earth magnesium/silicon ratio of 1.16 ± 0.01, and a mantle magnesium/silicon ratio of 1.25 to 1.28. The initial core would contain 3.5 to 4.1 weight % silicon, 2.9 to 3.1 weight % oxygen, 0.11 to 0.14 weight % magnesium, and 0.04 to 0.10 weight % hydrogen, along with sulfur and carbon. We predict that super-Earths can retain large metallic cores even with several weight % water.