<p>The Great Oxidation Event across the Archaean–Proterozoic transition was one of the most transformative environmental changes in Earth history. However, uncertainties remain about when and where it began. Here we synthesize the phylogenetic record of cyanobacteria and geochemical records of nitrogen and thallium isotopes and find converging evidence for oxygenated bottom waters on marine shelves in the Neoarchaean about 200 million years before the Great Oxidation Event. The O₂ was produced by benthic microbial mats, the dominant morphotypes of cyanobacteria at that time. Conditions were sufficiently oxidizing to stabilize nitrate and manganese oxides in sediments. Box modelling shows that micromolar levels of dissolved O₂ were attainable in this scenario under plausible Archaean conditions. The rise of O₂ was initiated on marine mud according to our synthesis. Productive Neoarchaean shelves may have been more oxidizing at the bottom than the top, consistent with the ‘upside down’ Archaean biosphere hypothesis.</p>