The Holocene sequence of the Humber Estuary displays a wide range of sediment types within which the preservation of microfossils is highly variable. Its evolution has been reconstructed using a range of environmental proxies with chronological control provided by more than 90 radiocarbon dates. Results are presented of diatom analyses from three cores typical of the inner, middle and outer estuary (HMB20, HMB7 and HMB12) and of three cores that illustrate the role of organic deposits (peats) and their associated pollen (HMB13, HMB12 and the Ancholme Valley) in the definition of sea-level index points. The reconstruction of relative sea-level change shows a rapid rise in the early Holocene, followed by a reduced rate of rise in the mid-late Holocene. This reconstruction, together with information on the pre-Holocene surface and the different palaeoenvironments from the cores have been integrated within a geographical information system and then interpreted to yield a series of palaeogeographical maps of the Humber at 1000-year time slices between 8 and 3 cal. ka bp. The marine transgression progressed up the estuary after 8 cal. ka bp, reaching the inner estuary by 6 cal. ka bp. The expansion of intertidal environments probably reached its maximum around 3 cal. ka bp. Changes since 3 cal. ka bp are described using archaeological and historical records. Tidal asymmetry is a major controlling factor on the balance of sediment accretion and erosion in the estuary. Sedimentary and bathymetric evidence suggests a damped oscillation between flood and ebb asymmetry in the Humber over the Holocene period. Such a conclusion would be of great importance to estuarine managers and users since it could be used to predict the future development of the estuary.