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Geochemical proxies indicate that atmospheric oxygen levels were <10–5 times present atmospheric levels (10–5 × PAL) until the start of the Great Oxidation Event (GOE; 2.33 Ga). However, trace metal and isotopic data from sedimentary rocks have been interpreted to reflect the presence of oxygenated surface oceans ≥2.5 b.y. ago, implying decoupling of the atmosphere and shallow marine systems. Evidence for oxygen in shallow oceans has fueled the idea that oxygenic photosynthesis evolved long before the GOE and that oxygen did not accumulate in the atmosphere because it was scavenged by reductants such as dissolved Fe2+, a process thought by some to have formed banded iron formations (BIFs). Here we present high-resolution microscopy showing that 2.45 Ga shallow-water BIFs were deposited as ferrous iron-rich muds dominantly composed of greenalite; these muds were rapidly cemented by silica on the seafloor, and subsequently eroded and redeposited as intraformational chert clasts. Our experimental results and kinetic models show that the accumulation of greenalite required seawater oxygen concentrations <10–6 × PAL on the shallow shelf. We infer that oxygen levels of the surface oceans and atmosphere were not decoupled 2.45 b.y. ago, but that both were exceedingly low (<10–5 × PAL). Our findings support the hypothesis that oxygenic photosynthesis evolved shortly before atmospheric oxygenation and was a direct cause of the GOE.