Phosphorus is an essential nutrient that is thought to have regulated primary productivity in global oceans after the advent of oxygenic photosynthesis. The prime source of seawater phosphorus is regarded to be continental weathering of phosphate minerals. Ancient seawater phosphorus concentrations have been constrained using the phosphorus content of iron-rich chemical sediments—banded iron formations (BIFs); however, the removal processes and depositional phases remain unclear. Here we report that nanometer-sized apatite crystals (<500 nm) are ubiquitous in 3.46-2.46 Ga BIFs and cherts from the Kaapvaal (South Africa) and Yilgarn, and Pilbara (Western Australia) cratons. The apatite is uniformly dispersed in a chemical sediment comprising greenalite nanoparticles, which were encased in very early diagenetic silica cement that limited compaction and chemical reactions. The lack of organic carbon (below detection; <0.3 wt%) and absence of primary iron oxides implies that the phosphorus was not derived from the degradation of organic matter or seawater scavenging by oxide particles. Instead, the occurrence of apatite in sediments derived from hydrothermally sourced Fe2+ and SiO2(aq) suggests that phosphorus too was derived from vent plumes. Today, seawater P is rapidly removed from vent fluids due to scavenging by oxidized Fe2+. However, prior to the Great Oxidation Event (2.45-2.32 Ga), dissolved phosphorus released during anoxic alteration of seafloor basalts escaped the iron-oxidation trap. Our results point to the existence of a submarine hydrothermal flux of dissolved phosphorus that supplied nutrients to the early anoxic oceans. High amounts of seawater P may help to explain why phosphorus is ubiquitous in cell biology—it was not limiting during the origin and early evolution of life.