Abstract: In China, river embankments often suffer from weak foundation conditions, making them susceptible to seepage, piping, and slope failures during flood seasons. Regular, rapid, and accurate inspections are essential for ensuring the safe operation of embankments. As an effective non-destructive geophysical technique, Ground Penetrating Radar (GPR) has been widely applied in the detection of potential hazards in embankments. However, raw GPR signals often contain considerable high-frequency noise and background interference, making it difficult to extract reliable features under complex field conditions. Traditional spectral analysis methods, such as the Fourier Transform, typically suffer from spectral smearing and unclear dominant frequency components, limiting their practical effectiveness. To address these limitations, this study proposes a 3D spectral energy ratio imaging method based on combined wavelet–Fourier transforms for detecting hidden hazards in embankments. In this approach, wavelet transform is first applied to analyze non-stationary and transient components of the radar signal, allowing for multiscale decomposition of its frequency characteristics. Subsequently, a short-time Fourier transform is used to calculate the temporal evolution of frequency-domain information and extract dominant frequency components and energy distribution across time windows. Based on this, a classification criterion of hazard types is constructed using the spectral energy ratio, enabling the effective separation of loose zones and water-enriched zones within the embankment. This approach facilitates high-resolution, efficient, and non-destructive identification of internal embankment anomalies. Finally, a field investigation was carried out on the Sanjiang Lianwei embankment in Yongxiu County, Jiujiang City, Jiangxi Province. The results demonstrate that the proposed method successfully detects and delineates loose and water-rich areas within the embankment body, providing strong technical support for hazard assessment and routine inspection of earthen dams.