Deep-water cherts are common in early Precambrian successions. Their mode of formation is unclear but proposed mechanisms include seawater silica precipitation, silica adsorption onto iron oxide particles and silica replacement of seafloor sediments. Here we document ≥80 laminated chert beds (0.02–7 m thick) in 2.56–2.49 Ga shelf sequences in drill-hole ABDP9 from the Hamersley Group, Australia. The laminated chert beds, including thin intervals of banded iron formation (BIF), are concentrated in six major intervals that first appear ca. 75 m.y. before deposition of the 2.49 Ga Brockman Iron Formation. The chert beds do not preserve textures indicative of seafloor replacement of precursor grains but of a chemical sediment comprising greenalite nanoparticles enclosed in silica cement with syneresis cracks that truncate sedimentary lamination. The greenalite is interpreted to have precipitated from dissolved Fe(II) and SiO2(aq) transported by hydrothermal plumes. Its ubiquity in laminated chert cement and the capacity of clay minerals to sorb silica, suggest the operation of a greenalite-silica shuttle by which excess dissolved silica in the seawater-plume mixture adsorbed onto settling Fe(II)-silicate nanoparticles. Upon deposition, pore-water silica concentrations surpassed the threshold for cementation due to the drawdown of silica into sediment pore waters and dewatering of underlying siliceous muds. In contrast, the lack of non-ferruginous chert beds in deep-water shelf sediments suggests that silica concentrations were lower in non-plume seawater. The appearance and disappearance of ferruginous cherts in shelf sequences is interpreted to record the waxing and waning of distal vent plumes. Deposition of chert beds starting at 2.56 Ga culminated with the development of thick, laterally extensive BIFs after 2.49 Ga, signalling enhanced ocean ridge volcanism and the transgression of vent plumes across a drowned shelf. The disappearance of basinal cherts and major BIFs after the Great Oxidation Event (2.45–2.3 Ga) may record the disruption or shutdown of the oceanic greenalite-silica shuttle.