The Kilmaluag and Skudiburgh Formations of the Bathonian, Great Estuarine Group, represent a unique palaeoenvironment within the British Jurassic. The Kilmaluag Formation is divided into two distinctive facies. The ‘clastic facies’ of N Skye comprises calcareous mudstones and shales, with subordinate sandstones and argillaceous limestones. The depositional setting was one of shallow, ephemeral lagoons, closed from the sea. Sublittoral lagoon, mudflat and channel environments are identified, and fossil faunas indicate low salinity. The ‘argillaceous limestone facies’ of southern Skye, Eigg and Muck, formed in a similar depositional setting, although sandstones are not present. Alternations of carbonate rocks (some dolomitic) and calcareous shales probably reflect palaeoclimatic fluctuations between humid and arid periods. The overlying Skudiburgh Formation is interpreted as being alluvial. Floodplain, channel and overbank deposits are identified by the presence of mottled mudstones, sands and lensoidal silts. Syndepositional carbonate nodules are interpreted as calcrete, which occasionally coalesced to form extensive hardpan calcrete horizons. The vertical facies sequence reflects a late Bathonian regression. The coastal plain, terrestrial environments of the Skudiburgh Formation were transgressed during the Callovian Stage, an event which ended paralic deposition in the Hebridean Jurassic.