A study of sound propagation over a submarine canyon northeast of Taiwan was made using mobile acoustic sources during a joint ocean acoutic and physical oceanographic experiment in 2009. The acoustic signal levels (equivalently, transmission losses) are reported here, and numerical models of three-dimensional sound propagation are employed to explain the underlying phsyics. 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 suggests that reflection from the canyon seabed causes three-dimensional sound focusing when the direction of propagation is along the canyon axis. 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.