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The relative height of the seafloor can be estimated by using two vertically displaced receivers. In this paper, we propose techniques to improve the accuracy of the estimated height. Our results are based on the use of synthetic aperture sonar (SAS) imaging, which implies coherent addition of complex images acquired from a moving platform. The SAS processing improves the along-track (or azimuth) resolution, as well as the signal-to-noise ratio (SNR), which in turn improves the estimated height accuracy. We show that the shift of the effective center frequency induced by coherent, frequency-dependent scattering affect the time-delay estimates from complex cross correlations, and we propose a correction technique for broadband signals with uneven magnitude spectra. To reduce the effect of geometrical decorrelation and increase the coherence between the images, we beamform the sonar images onto an a priori estimate of the seafloor height before correlating. We develop a mathematical model for the imaging geometry. Finally, we demonstrate our proposed estimators by providing relative seafloor height estimates from real aperture and SAS images, obtained during the InSAS-2000 experiment at Elba Island in Italy. In particular, we demonstrate that the SAS image quality is significantly improved by inclusion of the height estimates as a priori information.