After a phase of data collection, consisting of historical data and an in-situ measurement campaign organised by IMDC modelling team, numerical models have been developed to capture the tidal and wave characteristics in the bay and to simulate the sand and fine sediment transport in the estuary and navigation channel to the port of Guayaquil. The monitoring data set consisting of water level, flow velocity profiles, sediment concentration profiles and waves is extensively used for model calibration. It was shown the model reached a high degree of accuracy for hydrodynamics and sediment transport, and can be used for studying sediment dynamics in the estuary.