Knowledge of the structure of a flow is really significant for the proper conduct a number of industrial processes. In this case a description of a two-phase flow regimes is possible by use of the time-series analysis e.g. in frequency domain. In this article the classical spectral analysis based on Fourier Transform (FT) and Short-Time Fourier Transform (STFT) were applied for analysis of signals obtained for water-air flow using gamma ray absorption. The presented method was illustrated by use data collected in experiments carried out on the laboratory hydraulic installation with a horizontal pipe of 4.5 m length and inner diameter of 30 mm equipped with two 241Am radioactive sources and scintillation probes with NaI(Tl) crystals. Stochastic signals obtained from detectors for plug, bubble, and transitional plug – bubble flows were considered in this work. The recorded raw signals were analyzed and several features in the frequency domain were extracted using autospectral density function (ADF), cross-spectral density function (CSDF), and the STFT spectrogram. In result of a detail analysis it was found that the most promising to recognize of the flow structure are: maximum value of the CSDF magnitude, sum of the CSDF magnitudes in the selected frequency range, and the maximum value of the sum of selected amplitudes of STFT spectrogram.