The existence of a submerged landscape that may preserve Holocene material around the UK has long been postulated. In recent years, major advances in techniques of sea-floor and subsea-floor survey together with advances in GIS modeling have provided the foundation for the refinement of regional topography, different patterns of inundation and archaeological survival. Research has necessarily focused on the broadscale and relied on generalised modelled data in order to provide overall interpretation, but the challenge for archaeology is to approach human experience at a variety of scales down to the local level. The Orkney archipelago in the north of Scotland provides an ideal location to investigate the changing landscape of the early Holocene because of active relative sea-level rise, locations of sediment preservation and the nature of the archaeological remains. This paper presents the results of research at different scales from the general to the local. In this way we hope to generate discussion regarding analysis of the interplay between natural landscape change and human activity associated with the changing patterns of relative sea level that occurred throughout the Mesolithic and Neolithic. The results show that an interdisciplinary approach can provide valuable information to investigate human behavior in response to natural changes.