Sustainable management of coastal zones has become a complicated issue. The majority of the human population lives along the coast, where their activities, together with a range of environmental changes, have altered the natural ecosystem processes and caused changes in coastal wetlands. To ensure sustainable use of coastal resources, a comprehensive set of modelling tools can help managers to make decisions. This study uses Comerong Island (southeastern NSW, Australia) as a case study to demonstrate the importance of modelling modifications to environmental change. Several data-based modelling approaches are employed to explore how human activities have altered this estuarine island setting over the last sixty years (1949 – 2014). Multi-temporal changes in land cover, shorelines and sediment delivery are estimated from remote sensing data, GIS analysis, and laboratory tests on water and sediment samples (grain size, X-ray diffraction and loss on ignition and water analysis). Results show there are significant changes to the areal extents and elevation of mangroves, saltmarshes and shorelines in the wetlands on Comerong Island over the time period of analysis, including northern accretion (0.4 km2), eastern, middle and southern erosion (0.7 km2) of the island. The implementation of modelling using GIS tools, water and sediment samples to monitor ecosystem processes, such as sediment transport and erosion/deposition, will allow resource managers to make more informed decisions by evaluating the potential consequences of the existing situation.