Sedimentary phosphorites in Cambrian-Ordovician boundary beds in Estonia are among Europe's most extensive phosphate rock reserves, with a tonnage of approximately three billion tonnes. In addition, they are potential sources of rare earth elements and yttrium (REE + Y). The ore consists of sandstone rich in phosphatic brachiopod fragments deposited in a shallow marine peritidal environment of the Baltic Paleobasin. A detailed geochemical and mineralogical investigation was conducted on the northern part of the Toolse deposit based on three drill core cross-sections. The REE sequestration model was developed based on the correlation of the sedimentary facies of the members of the Kallavere formation. Analyses were conducted on 140 whole-rock samples and 14 discrete black shale samples. Inductively coupled plasma mass spectrometry (ICP-MS), X-ray fluorescence (XRF) and X-ray diffraction (XRD) measurements were performed for each sample. Textural analyses were conducted with field-emission scanning electron microscopy (FE-SEM), and quantitative wavelength dispersive spectrometer (WDS) analysis of major and trace elements was performed with an emission electron probe microanalyser (EPMA).The PAAS normalised REE + Y patterns were relatively homogeneous throughout the deposit except for the cerium and yttrium contents. The REE + Y contents of the phosphorites indicate a distinctive ‘bell-shaped’ pattern enriched with middle-REE (MREE) enriched. In the lower part of the deposit, the ∑REE + Y concentration is enriched up to 12-fold, compared to the average shale, reaching up to 1234 ppm. LREE enrichment is observed in these horizons, with a 9-fold peak at neodymium. In terms of absolute values, the most prevalent REEs are, in order, Ce, Y, Nd, and La, which respectively reach maximum mean values of 296 ppm, 248 ppm, 164 ppm and 135 ppm.The profiles indicate multistage uptake during transport, deposition, and early diagenesis of brachiopod detritus. The sedimentation was associated with a steep redox gradient in the porewater in a coastal environment during the beginning of marine transgression. The near-shore upwelling of oxygen-poor deeper water rich in dissolved nutrients and Mn, combined with the input of lithogenic Fe, helped create favourable conditions for REE sequestration. Positive Y anomalies indicate an initial uptake of REE + Y by hydroxyapatite through Ca substitution in an oxic environment near the sediment–water interface. The sediment burial induced the formation of carbonate fluorapatite (CAF) and a shift to the REE adsorption uptake mechanism, reinforced by the significant intercrystalline porosity of the shells. The transition to a suboxic environment below the surface layers resulted in the reductive dissolution of Mn-(oxyhydr)oxides and the release of LREE in the porewater system, resulting in an overprint of the original REE pattern to the point of inducing positive Ce anomalies. A late enrichment in MREE occurred during early diagenesis as a result of desorption of REE from the Fe-(oxyhydr)oxides and organic-rich particles under relatively anoxic conditions.
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