Investigation of shallow-marine environments for submerged prehistoric archaeology can be hampered in many localities by extensive bedrock exposure and thus limited preservation potential. Using the concept of ‘seamless archaeology’ where land-based archaeology is integrated across the intertidal zone through to the offshore, a multi-disciplinary approach is essential. This approach taken in the Bay of Firth, Orkney uses geophysics, historical archive and ethno-archaeology, coastal geomorphology, palaeo-environmental analyses and sea-level science, and allows a clearer understanding of the landscape in which prehistoric settlers lived. While acknowledging the limitations of the preserved environment, we are successful in identifying areas of archaeological potential on the sea-bed for both upstanding structural elements as well as sediment preservation that contains evidence for human occupation. This has wider implications beyond Orkney's World Heritage sites to provide a blueprint for similar studies elsewhere in the coastal zone.