Estuaries are influenced by both oceanic and catchment forcings are expected to be subject to more frequent and intense coastal storms and heavy rainfall on the southeast Australia coast due to climate change. General circulation models and dynamic downscaling indicate that the 20 year average recurrence interval (ARI) maximum daily rainfall would increase in the order of 25% in this region under the high emission future by 2090. Such increases in extreme rainfall are predicted to cause an average increase of 55% in the equivalent ARI flood discharge into the Georges River, which features one of the largest floodplains and urbanized areas in Australia. This study quantifies consequent changes in extreme estuary water levels using the hydrodynamic model RMA-2. Recorded rainfall and water level data from an observed 20 year ARI flood event occurred in March 2022 were used for model calibrations. Forced by the 20 year ARI historical and high emission future scenario flood conditions, RMA-2 predicts the future peak water levels will rise 1m in the upper estuary in the absence of changes in oceanic forcing. Sea level in the eastern Australia is predicted to rise by 0.66m under a high emission scenario. When combined with a predicted 20 year ARI barometric rise of 0.26m sea level rise, future flood peak water level are predicted to rise 1.3m in the upper estuary and 0.9m in the lower estuary at 20 year ARI. Consequently, under climate change, catchment floods dominate changes in peak water level in the upper estuary while oceanic processes principally determine changes in the lower estuary. The storm wind speeds are shown to have negligible impact on extreme water levels. Climate change storm impacts are predicted to have significant impacts on inundation of densely-populated regions, especially on Australian east coast.