Sonar data acquired by sub-bottom profilers and echosounder systems are widely used to estimate geoacoustic properties of marine sediments. However, the uncertainty of the seabed property estimates caused by water-column variability may limit the application. In this paper, the acoustic focusing and defocusing effects of nonlinear internal gravity waves on normal-incident acoustic reflection measurements are studied. The experiment data were collected in the South China Sea from two transceiver moorings located at two different sites, one of which contained strong nonlinear internal waves (NIWs), while another site did not. The observed reflection intensity variation at the internal wave site varied up to 10 dB. On the other hand, the bottom reflections at the other site without internal waves were stable, and a seafloor sediment sample collected there was analyzed to validate the sediment type inferred from bottom loss. Numerical simulations using ray-tracing and parabolic equation models confirmed the cause of this intensity fluctuation by the acoustic focusing and defocusing of NIWs. This study eventually showed that NIWs may induce a significant bias for geoacoustic property estimates from seabed reflection coefficients.