Finely laminated cherts enclosing nanoparticles of greenalite and apatite are ubiquitous in Archean-Paleoproterozoic (3.46–2.45 Ga) ferruginous cherts, jaspilites and Banded Iron Formations (BIFs) and the greenalite and apatite are considered to be primary deposits. The cherts and BIFs are chemical sedimentary rocks interpreted to have been precipitated in marine settings prior to the first permanent rise in atmospheric oxygen at the Great Oxidation Event (GOE) ca. 2.45–2.32 M.y. ago. As chemical sediments, they are potential archives of the solutions from which they precipitated, incorporating signals from hydrothermal fluids and ambient seawater. Previous studies of rare earth elements and Y (REY) in pre-GOE BIFs have mostly found an “Archean seawater signature” with positive Eu anomalies, attributed to the influence of high-temperature hydrothermal processes, and positive anomalies for La, Gd and Y, ascribed to seawater. REY abundances determined by in situ LA-ICP-MS are presented for well-preserved, laminated greenalite-bearing cherts from ten formations of pre-GOE ferruginous cherts and BIFs from Western Australia. The samples come from a wide range of depositional environments, e.g., submarine proximal volcanic environments, basin floor, slope and deep marine shelf, and are between 3.46 Ga to 2.45 Ga in age. Five groups with different REY patterns are identified, namely (i) mafic-volcanic-influenced vent-proximal chert from the Marble Bar Chert Member of the Duffer Formation of the Warrawoona Group; (ii) felsic volcanic- and sediment-associated chert from the Kangaroo Caves Formation of the Sulphur Springs Group and the Wilgie Mia Formation of the Murchison Supergroup, (iii) ferruginous cherts in shelf sediments from the Bee Gorge Member of the Wittenoom Formation of the Hamersley Group, (iv) BIFs from the Nammuldi Member of the Marra Mamba Iron Formation and Joffre Member of the Brockman Iron Formation, Hamersley Group, and (v) BIFs from the Dales Gorge Member of the Brockman Iron Formation. Of these, only the Dales Gorge Member BIF has a typical Archean seawater signature while the others have REY patterns likely reflecting differing source fluids and environments of deposition but not necessarily global ocean chemistry. Analyses of chert containing sub-micron-sized particles of greenalite and apatite indicate that the likely hosts of the REEs are apatite, siderite and possibly greenalite. The REY patterns of the greenalite-bearing cherts may differ from those of bulk samples of the same formations, perhaps reflecting a diagenetic overprint in the bulk samples, whereas the greenalite-bearing cherts likely preserve their depositional compositions, locked in by early silicification.