An organic carbon (Corg) and sulphur (S) storage inventory for Holocene sediments in the Humber Estuary is established; sources of organic matter and their variation over time are identified, and with chronological control, the importance of estuarine sediments as Corg and S stores is demonstrated. Humber Holocene sediments are grouped into seven widespread environmental facies with statistically significant geochemical data sets: (1) oak-hazel fenwood (OHF); (2) alder carr (AC), appearing as peats in core; (3) river channel muds or sands (Rcm/s); (4) high saltmarsh (HSM); (5) low saltmarsh (LSM); (6) intertidal mudflat (ITMF); and (7) a sandy facies (S). Carbon, nitrogen and sulphur (CNS) abundances show that these facies have diagnostic geochemical signatures and δ13C values for bulk organic matter exhibit a range of average values: −28‰ (terrestrial peats), −27‰ (HSM), and −24.5‰ (ITMF) reflecting the up core transition from terrestrial peats through saltmarshes to more open marine mudflat environments as regional sea-level rose. Chronology and average sedimentation rates are partly constrained by radiocarbon dates; palaeomagnetic techniques helped define discrete sediment packages and discontinuities (time gaps). Although the Humber Holocene sediment record is not continuous, long-term sedimentation rates (about 1 mm a−1) show that sediment accretion kept pace with regional sea-level rise between 6 and 2 cal. ka BP. This sedimentation rate, combined with core evidence to allow a geographic reconstruction of the palaeo-Humber (3–2cal. ka BP), is used to calculate storage values for Corg and S in the various environments of the palaeo-Humber. Comparison of the Corg and S sedimentation and storage terms for the palaeo-Humber with modern values highlights the impacts of reclamation and commercial/urban development in the estuary in the last 300 years. OHF and AC peats, which were the largest Corg and S stores in the palaeo-estuary, are now absent (reclaimed), while saltmarshes are no longer widespread. Conservative calculations show a net decrease in Corg deposition from about 3.2 × 105 tonne in the palaeo-estuary to no more than 2.5 × 103 tonne today, a >99% reduction in potential Corg storage capacity. The total modern yearly S deposition is approximately 2% of its value 2ka ago. Removal of saltmarsh and associated brackish-freshwater wetland suggests that suspended sediment and associated Corg and S are currently bypassing former (Holocene) storage areas and may be impacting North Sea biogeochemical cycling.