This is a dataset to accompany a paper submitted in April 2025 to Historical Biology: Miller, C. Giles and Jouet-Sarkany, Monique M. H. 2025. Sir John Murray’s H.M.S. Challenger Sedimentary Deposits Collection at the Natural History Museum, London. https://www.biorxiv.org/content/10.1101/2025.03.21.644325v1. A description of the fields is available via this link and the abstract for the paper copied: The Natural History Museum holds 4,713 bottles, tubes, boxes and slides containing sediment and derived preparations from the voyage of H.M.S. Challenger (1873-1876). The sediment collections include manganese nodules, pumice, and various marine vertebrates and invertebrates from all the major oceans of the world. A complete online database of the collection is presented to include all of the associated collecting and preparation data from the oceanic dredges, trawls, soundings and anchor mud collections alongside shallower water collections previously undocumented in the Challenger Deep Sea Deposits Report of Murray and Renard (1891). The dataset allows assessment of other Challenger sediment collections in museums and private collections. A historical account of the collection follows; collecting and studying onboard, studying in Edinburgh post cruise, donation by Sir John Murray’s family to the British Museum (Natural History) and accounts of the collection’s historical housing at the museum. The historical context and presented dataset are intended to aid future users of the collection to select suitable materials for study or display. A review of previous scientific and exhibition uses of the collection is followed by suggestions for the future storage and potential for illuminating the debate on anthropologically driven climate, biodiversity and atmospheric changes.