Monitoring estuarine ecological-geomorphological dynamics has become a crucial aspect of studying the impacts of climate change and worldwide infrastructure development in coastal zones. Together, these factors have changed the natural eco-geomorphic processes that affect estuarine regimes and comprehensive modelling of coastal resources can assist managers to make appropriate decisions about their sustainable use. This study has utilised Towamba estuary (southeastern NSW, Australia), to demonstrate the value and priority of modelling estuarine dynamism as a measure of the rates and consequences of eco-geomorphic changes. This research employs several geoinformatic modelling approaches over time to investigate and assess how climate change and human activities have altered this estuarine eco-geomorphic setting. Multitemporal trend/change analysis of sediment delivery, shoreline positions and land cover, determined from fieldwork and GIS analysis of remote sensing datasets, shows significant spatio-temporal changes to the elevation and areal extent of sedimentary facies in the Towamba estuary over the past 65 years. Geomorphic growth (~ 2600 m2annually) has stabilised the estuarine habitats, particularly within native vegetation, salt marsh and mangrove areas. Geomorphic changes have occurred because of a combination of sediment runoff from the mostly unmodified terrestrial catchment, nearshore processes (ocean dynamics) and human activities. The construction of GIS models, verified with water and sediment samples, can characterise physical processes and quantify changes within the estuarine ecosystem. Such robust models will allow resource managers to evaluate the potential effects of changes to the current coastal ecosystems.