A novel method of structural damage detection, aimed at monitoring the state of a structure based on measured time series data, is presented for the analysis and interpretation of underwater explosion (UNDEX) test data. This method extracts sets of simple basis function components, known as Intrinsic Mode Functions, and tracks structural damage based on a fundamental relationship connecting the instantaneous phases of measured structural waveforms to the structural mass and stiffness parameters. The data were obtained during a recently conducted test series in which shock isolators, mounted on an adjustable deck fixture, are used to mitigate the shock impact for equipment cabinets. The state of the isolation system is then evaluated, and possible structural damage is identified based on instantaneous attributes such as the frequency of structural response and the phase of structural waveforms. The studies presented here show that this method, intrinsically suited to non-linear systems and non-stationary processes, produces valuable insight into the state of a structure during an extreme loading event. It can be used to assess structural conditions directly from recorded UNDEX data.