Coastlines are dynamic environments, with their Eco-geomorphology controlled by a complex range of natural and anthropic processes. Estuarine environments and associated wetland ecosystems are a critical shoreline types with regards to biodiversity, and are particularly susceptible to the influence of sea-level rise. This project applied future sea-level rise of Intergovernmental Panel on Climate Change (IPCC) hydro-scenarios to assess its impact on the eco-geomorphic aspects of coastal ecosystems in terms of risk assessment and sustainability. Comerong Island is used as a case study and is compared with other surrounding ocean-influenced and lagoonal deltas to assess the regional effects of sea-level rise. Applying the IPCC scenarios to the chosen geomorphic coastal data-sets resulted in a hydro-geomorphic model that shows the study site was already under pressure in 2015, with significant land area projected to be lost by 2050 and 2100. These findings are also expected to occur across the remaining estuaries in southeastern Australia. Applying this broad-scale, multi-strand application of geoinformatics simulation (GIS & RS), together with the various IPCC sea-level rise scenarios, will be necessary to assess future ecosystem sustainability management plans for coastal zones worldwide.