The erosion of the river bed material at bridge pier foundation produced by scour events is one of the main causes of the observed masonry bridges failures and collapses. Foundation settlements and rotations derived from the reduction of the footprint under the piers threaten masonry arch bridges integrity more than any gravity load. The resulting effect on the structure is the development of cracking mechanisms on the arches which may affect the dynamic behaviour of the whole bridge. A scaled experimental model of a masonry arch bridge has been built in the laboratory of the Dep. of Structural Engineering at the Politecnico di Torino. The aim was to better understand scour damage scenario and to identify early structural symptoms of pier erosion. A preliminary dynamic identification is carried out on the intact structure and a comparison with the FEM results is performed. The set of identified modal parameters is adopted as the reference system that will be compared with those acquired after the application of damage of increasing extent.