Understanding the drivers of vertebrate fossil preservation is important for paleontologists who rely on well-preserved fossils to study the biological or ecological context of the fauna they represent. Differences in preservation limit the ability to compare biological or ecological change across time. Bones, however, can contain clues of their preservational history: natural voids in skeletal remains are potential sites of mineral precipitation during early and late diagenesis, and the reactive bioapatite provides chemical and physical signals of the postmortem environment. The sensitivity of both infilling minerals and taphonomic alteration to the post-mortem environment has yet to be tested in the fossil record. Bones associated with discontinuity surfaces such as hiatal flooding surfaces and erosional sequence boundaries should face prolonged exposure at the sediment-water interface and/or within the surface mixed layer, increasing the opportunity for modification by taphonomic processes and geochemically disparate (redox) conditions, compared with bones from facies within aggradational intervals, where burial is most likely to be rapid and immediately permanent. µXRF and thin-section-based petrographic analysis of marine mammal bones from the famously fossiliferous Eocene siliciclastics of Wadi al-Hitan, Egypt, reveal strong variation with stratigraphic position: bones found along the sequence boundary show Fe-oxide linings and evidence of desiccation and subaerial exposure, distinct from bones of other settings; a bone from the maximum flooding surface uniquely lacks calcite but has brecciated cancellous bone; bones from systems tracts are variable in the extent of infill but show calcite microfacies consistent with exclusively subaqueous and specifically shallow marine deposition. Early diagenetic signatures were preserved despite many fossil specimens being strongly fractured and infilled by gypsum precipitated during weathering. Bones and their abundant pore space thus acted as time-capsules of early diagenetic conditions, retaining authigenic minerals and other microtaphonomic features linked to their original (Eocene) depositional context.