The application of a sequence stratigraphic approach to the study of the Middle and Upper Jurassic of the Moray Firth has enabled the stratigraphy of disparate onshore and offshore successions to be linked and clarified. The results allow for the construction of regional correlation panels, chronostratigraphic diagrams and palaeogeographic maps which illustrate the tectono-stratigraphic evolution of the basin and importantly show a new flooding history for this arm of the North Sea rift system. It is now demonstrable that the Inner Moray Firth (IMF) and Outer Moray Firth (OMF) were separated by a topographic high centred around the Ross Granite area (UKCS blocks 13/28 and 13/29) from the Bajocian until the latest mid-Oxfordian. New biostratigraphic results demonstrate that the first marine influx into the Buchan Trough area of the OMF was Callovian in age (significantly earlier than previous models) and probably marked connection with the South Viking and/or North Central Grabens. Similar marine depositional systems are envisaged to have developed in the geographically isolated IMF basin and Buchan Trough area of the OMF basin during the Callovian, early and mid-Oxfordian. The unification of these marine basins occurred during the latest mid-Oxfordian via the South Halibut Trough, with a subsequent early Kimmeridgian connection via the Halibut Platform. The new flooding model suggests that the drowning of the rift arm was more rapid than previously believed and that within the rift itself any relief associated with a Mid-Jurassic doming episode, which created ‘the Mid-Cimmerian Unconformity’ had effectively diminished by this time. Although the deflation of a triple junction-centred dome remained an important process in the basin’s Mid-Jurassic evolution it was not the sole causal control on rift-arm stratigraphy. Instead the complexities of the Mid- and Late Jurassic flooding of the Moray Firth are interpreted to be the result of both short- and long-term regional sea-level changes superimposed upon a complex evolving rift topography.