Evaluation of localized and distributed in time spectral energy in wave–current coexisting environment is investigated in this study. In order to understand the inherent characteristics of the flow under consideration, the Hilbert-Huang transform (HHT) is introduced to determine the instantaneous frequency corresponding to the maximum energy carrying by the velocity field. This frequency is associated with the timescale of the most energetic velocity fluctuations. The intrinsic mean frequency of the intrinsic mode function (IMF) is reduced with the increase in the IMF number. It was shown that the maximum energy is concentrated close to the center of the IMF series. The spectral characteristics obtained by the HHT are carefully compared with those obtained by more conventional Fourier and wavelet transform (FFT and WT, respectively). Addition of the surface wave component to the velocity field of the current-only case leads to the extension of the frequency range containing the dominant portion of the energy.