This paper presents an innovative method for scour monitoring, based on the analysis of the dynamic response of a bridge pier embedded in the riverbed. Apart from the mechanical and physical characteristics of the pier itself, soil-structure interaction (SSI) has an impact on the dynamical behaviour of the system. This is particularly the case for eigenfrequencies of the pier which decrease when the free length increases. In this paper, analytical developments are carried out for an Euler–Bernoulli beam, modelling the pier which is embedded in the soil with Winkler springs for SSI. By using Hamilton’s principle and endowing the specific boundary conditions, the system frequencies are assessed by looking for roots of the characteristic equation of the system. These eigenfrequencies are then compared with those of an equivalent cantilevered beam, which can be expressed analytically. Moreover, experiments are carried out to validate the concept of equivalent length as a parameter of the inverse problem, linking the dynamic behaviour of the system and the embedded length.