The first detailed investigation of a deep, coastal, sedimentary basin in Orkney reveals a complex Holocene history of back-barrier morphodynamics. At Scapa Bay, the sea flooded a freshwater marsh after ca. 9400 yr BP at ca. À5.4 m OD. Before ca. 7800 BP, abundant sediment from nearby cliffs was mobilised inland into a series of gravel barriers across the valley mouth. By ca. 7500 BP, direct marine influence was restricted in the back-barrier area, although saltmarsh persisted until ca. 5900 BP. By then, at least four gravel ridges had enclosed the backing lagoon, where freshwater inputs became dominant. As terrestrial sediments filled the basin, another freshwater marsh developed. The multiple barrier complex demonstrates progradation resulting from continuous sediment supply in a sheltered embayment. The progressively rising height of the barrier crests seawards probably resulted from a combination of factors such as barrier morphodynamics, increased storminess and long-term rising relative sea levels. The dominant vegetation surrounding Scapa Bay changed from open grassland to scrub ca. 9400 BP, then to deciduous woodland ca. 7800 BP, and to dwarf-shrub heath ca. 2600 BP, the latter probably a response to a combination of climate change and human activity.