Acoustic propagation measurements are made in a highly variable and stratified estuary using high frequency transducers (120kHz) on tripods placed across the main channel of the river flow. The measurements are taken in the Connecticut River across several tidal cycles, when the flood tide causes a wedge of seawater to press up the river bed, beneath the fresh water, and then be eroded and pushed back out during the ebb. BELLHOP, implemented via Matlab, is a beam/ray tracing method and is used to model the acoustic propagation in this environment using collected temperature, salinity, and depth data. Multiple modeling comparisons are done over the period of three full tidal cycles, totaling a thousand separate modeling runs and compiled into a time series. Arrival times measurements from the transducer system were able to be accurately modeled, validating BELLHOP as a useful tool in modeling this very dynamic and challenging acoustic environment.