Systems and methods for tracking dynamic structure in physiological data are provided. In some aspects, the method includes providing physiological data, including electroencephalogram (“EEG”) data, acquired from a subject and assembling a time-frequency representation of signals from the physiological data. The method also includes generating a dynamic model of at least one non-stationary spectral feature, such as at least one non-stationary spectral peak, using the time-frequency representation and a user indication, and applying a dynamic model of at least one non-stationary spectral feature in a parameter estimation algorithm to compute concurrent estimates of spectral parameters describing the at least one non-stationary spectral feature. The method also includes tracking the spectral parameters of the at least one spectral feature over time.