The Harbor Bay Isle residential project in Alameda, CA, USA, comprises some 600 acres (243 ha) reclaimed from the margin of San Francisco Bay underlain by very soft (C c ∼ 1), high-water-content clay (e 0 > 2): San Francisco Bay Mud. Settlements of as much as 2.5 m developed from about 7 m (varying across the site) of sandfill surcharge, with records over some 43 years extending through primary consolidation and into secondary consolidation (creep). Iterative numerical modelling using large-strain theory (implemented in the Microsoft Excel software program), constrained by in situ void ratios and oedometer trends, achieved close matches with settlement histories over the full 43 years for the three locations considered, each of which displayed a markedly different history from the others. The presence or absence of a dried ‘crust’ was found unimportant; instead, the proportion of subunits within the Bay Mud controlled the evolution of settlements. Subunits within Bay Mud, evident in modern cone penetration test soundings (which were not available during the reclamation works), exist across the region and have systematically different states and properties. Further, while ageing is a factor, depositional conditions of the Bay Mud have produced a residual fabric that presents as a component of the pre-consolidation pressure.