As the main component of a ballasted railway system, railway ballast is frequently used by the railway industry to enhance constructability and practicality. Numerous studies into train–track interactions focused on ballast modelling and idealisation in completely dry environments, but recent studies have found that, in extreme weather such as floods, water can clog natural ballast beds and change the initial state of their properties. Ballast models used in multi-body simulations have been mostly developed based on the instrumented impact hammering method considering the ballast as a spring/dashpot. The single degree of freedom (SDOF) idealization for ballast enables a non-destructive field testing technique for monitoring of railway components in practice. In this study, the suitability of the idealization of ballast for dynamic characteristics has been evaluated. A series of experiments have been performed with a variety of ballast conditions in flooding levels from 0 to 40 cm, with a frequency range of 0–500 Hz. The results clearly show that the increase in the flood level will result in increasing dynamic damping of more than 50% of dry natural ballast whilst reducing its stiffness and natural frequency. The novel insights are of great significance for exploring the non-linear dynamic traits of ballast in extreme environments, which can be integrated into the coupled train–track analysis that can better express more realistically the dynamic train–track interaction and load transfer mechanism of flooded railway tracks.