Global climate change has been identified as one of the major factors that could potentially alter the duration and timing of floodplain inundation and the hydrological connectivity between floodplain waterbodies. This study simulated potential changes in flow regimes and hydrological connectivity under the historical climate and projected future climates in the Fitzroy catchment (WA), a high conservation value aquatic ecosystem in northern Australia. The study was conducted using hydrodynamic modelling in conjunction with remote sensing and GIS. Simulated inundation information was combined with land topography data to quantify connectivity between wetlands and the Fitzroy River. Given the very large number of wetlands on the Fitzroy floodplain, 30 off-stream wetlands were investigated for connectivity based on their importance to fish biota. Connectivities were quantified for three different floods, ranging from a mean annual flood to a 20-year return period flood under present climate and predicted future climate for 2050. Hydrology, topographic relief and river bank elevation were found to be key factors controlling the level of connectivity. Under a wetter future climate the length of time wetlands were connected to the main river channel increased up to 16% and under a drier climate the wetland connectivity was simulated to decrease by 27%. The projected level of connection of individual wetlands under the historical climate and project future climate provides useful information to future studies on the movement and recruitment patterns of aquatic biota, wetland habitat characteristics and water quality, and biodiversity of individual wetlands