Abstract The diagenesis of lower Eocene shallow water carbonates with flint was studied in the Gebel Rewagen area, Eastern Desert, Egypt. The carbonates are mainly wackestones to packstones with benthic bioclasts embedded in a dark red luminescent micrite matrix. The studied succession displays a complex diagenetic history that involves syngenetic and late diagenetic processes. Silica, which exists either as persistent bands, nodules and/or silicified benthic bioclasts shows a distinctive pattern regarding its distribution, source, depositional environments and timing. Three lines of evidence support a syngenetic origin of the chert bands: (1) they alternate in a cyclic manner within the host carbonates and (2) they exhibit noticeable lateral persistence throughout the investigated area following the strata boundaries and (3) there is a lack of any carbonate dissolution in limestone adjacent to chert bands. The deposition of silica bands in association with shallow water carbonates is possibly related to eustatic sea-level changes, which were accompanied by episodic variations in silica and carbonate productivities. With a relative sea-level fall and the establishment of a lowstand period at the end of the early Eocene, a basinward shift of the groundwater zones is expected within the carbonate platform. During this period some late diagenetic processes took place, which involve: (1) the formation of siliceous and carbonate concretionary growths, (2) partial silicification of bioclasts, (3) neomorphic stabilization of the CaCO3 bioclasts and (4) the formation of equant calcite cement. Siliceous and carbonate concretions are believed to have taken place within microenvironments created and controlled by sulphate-reducing bacteria and physico-chemical and kinetic factors near a marine-meteoric water mixing zone. This is inferred from the distribution of iron sulphides, the non-ferroan nature of all concretions and the depleted δ13C (−5.4‰ to −6.0‰ PDB) and δ18O (−5.8‰ to −6.8‰ PDB) values of the carbonate concretions. The silica fabrics of all the partly silicified benthic bioclasts, with abundant pyrite cubes, argue for a delayed silicification process within the sulphate reduction zone. The close and relatively depleted δ18O values of the low−Mg calcite micrite matrix (−3.0‰ to −4.4‰ PDB) and benthic bioclasts (−3.4‰ to −4.8‰ PDB) indicate that both matrix and bioclasts have probably suffered neomorphic stabilization from freshwater-dominated solutions. The initial marine δ13C values of both low-Mg calcite matrix (+0.2‰ to −2.2‰ PDB) and altered benthic bioclasts (−0.2‰ to −0.9‰ PDB) are retained and not affected by diagenesis. The luminescence character and the extremely depleted oxygen values (−8.3‰ to −10.1‰ PDB) of the equant void-filling calcite mosaics are consistent with their formation within a meteoric phreatic realm.
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