In 2004, preparation for the nomination of the Prehistoric Pile Dwellings around the Alps to the UNESCO World Heritage List identified several specific objectives. The main objective was to obtain national and international recognition for the importance of this outstanding heritage and its contribution to knowledge of the Neolithic and the Bronze Age. These sites represent critical periods in the prehistoric development of regional cultures around the Alps. Inscription was sought to ensure better protection and conservation of these very fragile archaeological sites, which are increasingly threatened by natural phenomena and human activities. In addition, preparation for nomination to the World Heritage List focused on synthesising and disseminating knowledge of this heritage while promoting collaboration between researchers working on new and existing areas of research in the six countries engaged in this project. The balance required between the conservation of the integrity of the sites and further enquiry-based research was soon at the centre of discussions and emerged as an area of potential conflicting interests and viewpoints. UNESCO World Heritage inscription requires the protection of integrity (wholeness and intactness), yet there is a need to continue the excavation and sampling of these sites, not just to monitor their state of conservation but also to improve existing knowledge and clarify interpretation. This article seeks to examine and provide a potential basis to resolve this contradiction and to propose a new management model to reconcile protection of heritage and archaeological research.