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Abstract Laminated sediments can record seasonal changes in sedimentation of material from anoxic waters, including minerals of the redox‐sensitive elements Fe, Mn, and S that form under varying oxygen levels, mineral saturation conditions, and from microbial metabolism. However, preserving the oxygen‐sensitive minerals for identification is challenging when preservation of the spatial arrangement of laminae is also required. In this study, we compare methods for embedding sedimentary materials from anoxic waters and sediments from Brownie Lake, Minnesota, USA for analysis of the speciation for Fe, Mn, and S using synchrotron‐based X‐ray absorption near edge spectroscopy (XANES). We found that acetone dehydration and resin replacement in a 100% N₂glovebox successfully preserved the speciation of Fe and Mn minerals within laminated sediments. However, acetone removed some sulfur species from sediments, and epoxies contained sulfur species, which challenged identification of native sulfur species. Results from this study will aid researchers who are interested in spatial analysis of oxygen sensitive sediments, soils, or microbial mats in choosing a preservation method.