Abstract: The shifting footprint effect significantly degrades bathymetric accuracy in the nadir region of bathymetric side-scan sonar (BSSS), thereby limiting improvements in depth measurement precision and operational range. To address this issue, this paper integrates multi-subarray processing with resampling techniques and proposes a novel method. The approach first estimates seabed orientation preliminarily. Subsequently, a resampling-based registration operation is incorporated into the subarray beamforming process. Finally, the high-resolution Matrix Pencil (MP) method is applied to achieve precise seabed detection. Simulation results demonstrate that the proposed algorithm effectively mitigates the adverse effects of the shifting footprint phenomenon. Lake trial data show that the algorithm significantly enhances bathymetric performance in the nadir region, yielding an average reduction in relative depth measurement error of up to 150%. These results indicate that the proposed algorithm synergistically combines the robustness of beamforming with the high angular resolution of advanced estimation methods, thereby effectively increasing both the effective swath width and the depth measurement precision of current BSSS systems.