This study discussed conflicts in a large-scale development project realized in an archaeological area. The dam reservoir of Yortanli constructed as a part of a contemporary irrigation project in Western Turkey conflicted with the antique settlement of Allianoi, which had developed in the same area around a natural thermal spring in the 2nd century ad. The aim was to present the protection decisions and implementations related with the archaeological site of Allianoi in the Yortanl Dam Reservoir so that monitoring and criticism of its consequences can be possible in the future. The tools of the three disciplines, hydraulic engineering, structural engineering and conservation, were emphasized. The following conclusions were derived: The understanding of the protection-development conflict of archaeological heritage-dam relations in the case of Allianoi-Yortanl necessitates the evaluation of its legal, administrative, technical, and managerial aspects with all related governmental and non-governmental parts. The presented evaluation provides an opportunity for the discussion of the validity of the protection intervention, which is reburial of the remains prior to water retention in the dam, within an international framework. The presentation of the details of the protection process may facilitate the monitoring and criticism of its consequences in the future.