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A study of sound propagation over a submarine canyon northeast of Taiwan was made using mobile acoustic sources during a joint ocean acoustic and physical oceanographic experiment in 2009. The acoustic signal levels (equivalently, transmission losses) are reported here, and numerical models of 3-D sound propagation are employed to explain the underlying physics. The data show a significant decrease in sound intensity as the source crossed over the canyon, and the numerical model provides a physical insight into this effect. In addition, the model also suggests that reflection from the canyon seabed causes 3-D sound focusing when the direction of propagation is along the canyon axis, which remains to be validated in a future experiment. Environmental uncertainties of water sound speed, bottom geoacoustic properties, and bathymetry are addressed, and the implications for sound propagation prediction in a complex submarine canyon environment are also discussed.