Compound flooding events receive great attention due to their amplified flood risk when river flooding and storm surge occur simultaneously. With evidence of climate change increasing the frequency and intensity of extreme events, predicting the response of estuarine sediment dynamics and morphodynamics during compound flooding events under future scenarios becomes a challenge. Dynamical downscaling is a modelling tool that utilizes a high-resolution model to dynamically translate large-scale climate processes into finer regional domains in a coherent and dynamical manner (Jin et al., 2021). CMIP6 models were downscaled to GBR4 model to resolve the coral sea circulation impacting the Great Barrier Reef. GBR4 model was further downscaled to regional model to provide boundary conditions for estuarine model simulations. The compound flooding event, defined as the 99th percentile of river flooding concurrent with the 99th percentile of storm surge event, was extracted from GBR4 10yr-historical and 10yr-forcast simulations. These forcings were applied to drive an estuarine model for predicting sediment dynamics. Comparing sediment transport in historical and future compound events revealed changes in sediment transport behaviour and erosion/deposition patterns in greater spatial details within the estuary.