As part of the Office of Naval Research (ONR) sponsored Windy Island Soliton Experiment (WISE), two deep water moorings were placed in the northeastern portion of the South China Sea deep basin to conduct an acoustic propagation study. For approximately one year the source and receiver transmitted and received phase-modulated signals to measure the multi-scale variability in the transmission loss induced by the ocean mesoscale variability and the progression of internal tides and waves. A numerical acoustic propagation model based on Hamiltonian ray tracing is utilized to replicate the observed basic arrival structure and transmission loss. Being able to accurately model the basic arrival structure is a necessary first step before modeling the observed variability can be attempted. The comparison of the modeled arrival structure with the actual data was utilized to refine the angular resolution of the ray fan in the model, estimate the geo-acoustic properties of the bottom, and develop transmission loss estimates. Transmission loss measurements from sono-buoy data were used as an independent metric to evaluate the model.