This paper presents a new model for the palaeogeography of an important archaeological region in northern Scotlandthe former Loch Spynie, Moray. The method employed refines existing glacio-isostatic adjustment and relative sea-level models for the Holocene with open data sources of geomorphological, geotechnical and archaeological data to constrain the proposed former extent of marine, estuarine and other wetland environment through time. The study area is shown to be an important isolation basin that is highly likely to preserve dateable relative sea-level index points. The resulting palaeogeographic model for the former Loch Spynie estuary is then used to develop an archaeological narrative of coastal and maritime activity in later prehistory critiquing and supporting an emergent paradigm in understanding later prehistory in northern Scotland. This study demonstrates how it is possible to develop palaeogeographic models at scales useful for site-based archaeological interpretation bridging a problematic gap in archaeological narratives.