The World Heritage Sites of Orkney, Scotland contain iconic examples of Neolithic monumentality that have provided significant information about this period of British prehistory. However, currently, a complete understanding of the sites remains to be achieved. This is, in part, because the monuments lack an adequate context within the broader palaeolandscape. Recent investigations (seismic geophysical survey, microfossil analysis and 14C dating) in and around the Brodgar Isthmus, both onshore and offshore, are used to reconstruct the landscapes at a time when sea-level, climate and vegetation were different to that experienced today. Results show that in the early Neolithic the isthmus between the Ring of Brodgar and Stones of Stenness was broader with a smaller loch to the west. Furthermore this landscape contained sandstone outcrops that would have provided a potential source of stone for monument construction. Microfossil analysis and radiocarbon dates demonstrate that the Loch of Stenness was transformed from freshwater to brackish during the early Neolithic, perhaps immediately preceding construction of the major monuments. Finally, the analysis of our data suggests that sediment influx to the loch shows a tenfold increase coincident with widespread vegetation change that straddles the Mesolithic/Neolithic transition at c. 6 ka cal. B.P. These results provide, for the first time, a landscape context for the Neolithic sites on the isthmus.