The geomorphology of the present day and Holocene (3000 years ago) Humber estuary, United Kingdom, are described. More than 90% of the intertidal area and sediment accumulation capacity of the estuary has been lost to reclamation over this period. A similar situation prevails in many other urbanized estuaries. Nutrient budgets for the modern estuary are presented demonstrating little trapping of nutrients, due to the loss of intertidal areas. A speculative budget for the Humber during the Holocene is constructed, which suggests that the estuary was then an efficient sink for nitrogen and phosphorus. A budget is presented describing how nutrient cycling might operate in the Humber with contemporary nutrient loadings, but with the pre-reclamation geography. This suggests that in this form the estuary would significantly attenuate nutrient fluxes to the North Sea. The results are discussed in terms of options for managed realignment of estuaries in response to predicted sea-level rise.