A sequence stratigraphic framework for the late Jurassic Kimmeridgian and Bolonian stages of the Wessex–Weald Basin, southern England is proposed, based on the integration of sedimentological, geophysical and geochemical data. The NERC-funded Rapid Global Geological Events (RGGE) boreholes of Swanworth Quarry 1 and 2, and Metherhills 1, are used as reference sections. Eleven complete depositional sequences and their component systems tracts are recognized within the Kimmeridge Clay Formation, bounded by 12 sequence boundaries (Km1–12). Seventy-four boreholes have been used in this study. During the Kimmeridgian, a major transgression, associated with tectonic movements, led to a marked change in basin geometry. Major deepening of the sea during the late Kimmeridgian (Eudoxus Zone) led to a change from unconformities of basinwide extent to those confined to the basin margins. The progressive deepening of the basin towards a highstand in the mid-Bolonian (Wheatleyensis to Pectinatus zones) was associated with a broad-scale change in sedimentary, faunal and geochemical characters. The ‘layer-cake’ basin architecture and thickening of the Kimmeridge Clay Formation towards the basin centre suggests a dominantly aggradational system. The partially enclosed nature of the Kimmeridgian and Bolonian seas generated basin dynamics more analogous to those of modern day meromictic lakes. Consequently, sequence stratigraphic approaches derived from continental shelf-margins are inappropriate in epicontinental basins of this type.