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In this paper, we quantify the dynamical causes and uncertainties of striking differences in acoustic transmission data collected on the shelf and shelfbreak in the northeastern Taiwan region within the context of the 2008 Quantifying, Predicting, and Exploiting Uncertainty (QPE 2008) pilot experiment. To do so, we employ our coupled oceanographic (4-D) and acoustic (Nx2-D) modeling systems with ocean data assimilation and a best-fit depth-dependent geoacoustic model. Predictions are compared to the measured acoustic data, showing skill. Using an ensemble approach, we study the sensitivity of our results to uncertainties in several factors, including geoacoustic parameters, bottom layer thickness, bathymetry, and ocean conditions. We find that the lack of signal received on the shelfbreak is due to a 20-dB increase in transmission loss (TL) caused by bottom trapping of sound energy during up-slope transmissions over the complex and deeper bathymetry. Sensitivity studies on sediment properties show larger but isotropic TL variations on the shelf and smaller but more anisotropic TL variations over the shelfbreak. Sediment sound-speed uncertainties affect the shape of the probability density functions of the TLs more than uncertainties in sediment densities and attenuations. Diverse thicknesses of sediments lead to only limited effects on the TL. The small bathymetric data uncertainty is modeled and also leads to small TL variations. We discover that the initial transport conditions in the Taiwan Strait can affect acoustic transmissions downstream more than 100 km away, especially above the shelfbreak. Simulations also reveal internal tides and we quantify their spatial and temporal effects on the ocean and acoustic fields. One type of predicted waves are semidiurnal shelfbreak internal tides propagating up-slope with wavelengths around 40-80 km, horizontal phase speeds of 0.5-1 m/s, and vertical peak-to-peak displacements of isotherms of 20-60 m. These waves lead to v- - ariations of broadband TL estimates over 5-6-km range that are more isotropic and on bearing average larger (up to 5-8-dB amplitudes) on the shelf than on the complex shelfbreak where the TL varies rapidly with bearing angles.