Ground-penetrating radar (GPR) is a well-respected, effective, and efficient geophysical technique. However, for underwater engineering detection and underwater archaeology, the measured B-scan profiles typically contain surface-related multiple waves, which can reduce the signal to noise ratio and interfere with the interpretation of results. SRME is a feedback iteration method based on wave equation, which is frequently utilized in marine seismic explorations but very rarely in GPR underwater engineering detection. To fill this gap, we applied SRME to suppress multiples that appear in GPR underwater images. When we compared the effectiveness of the underwater horizontal layered model and the underwater undulating interface model, we found a high match rate between the predicted and the real-world multiples. In addition, the addition of the Gaussian random noise level with a 4% maximum amplitude to the B-scan profile of the horizontal stratified model yielded satisfactory multiple suppression results. Finally, we applied this method to the B-scan GPR section of actual underwater archaeological images to achieve multiple suppression, which can more effectively weaken and inhibit the surface-related multiples. Both numerical simulations and actual field data show that the SRME method is highly suitable for interpreting waterborne GPR data, and more accurate interpretation can be obtained from the GPR profile after multiples suppression.