This paper presents a shallow water depth estimation methodology using S-band Synthetic Aperture Radar (SAR) data from the HJ-1C satellite. It is based on the shoaling and refraction of long surface gravity waves as they propagate shoreward. A two-scale Bragg scattering model is used to describe the imaging process of long waves by SAR. By computing the Fast Fourier Transformation (FFT) for the selected sub image, wavelength and direction of the long wave can be retrieved from the two-dimensional (2D) spectra with wave tracking technology. Shallow water depths are then obtained from the linear dispersion relation with the calculated angular wave frequency obtained from other sources or first guesses of initial water depths or wave periods. Applicability and effectiveness are tested in the near-shore area of the Fujian province, China. Comparison between the derived results and water depths from an Electronic Navigational Chart (ENC) indicates that HJ-1C SAR is capable of higher resolution underwater topography detection, and the methodology can be used for shallow water depth estimation with good accuracy. The average absolute error and average relative error of the estimated results is 0·86 m and 11·05%, respectively.