Abstract: Wetlands are important habitat for many aquatic biota. Hydrological connectivity between wetlands and river channels through episodic floods is considered one of the key driving mechanisms for habitat quality and biodiversity in a river-floodplain ecosystem. The high biodiversity found in many unregulated floodplain systems are thought to be largely dependent upon these episodic floods. The Fitzroy River in Western Australia is one of Australia’s largest unregulated river systems and supports a large number of wetlands of known ecological and environmental value. An important issue for the management of these wetlands is to acquire knowledge of the extent, timing and duration of their connectivity to the river system. Likely potential climate changes in the future, will in turn change river flows and flood frequency and may affect wetland connectivity. As part of the Northern Australia Water Resource Assessment project, the hydrological connectivity of floodplain wetlands in the Fitzroy catchment was investigated. The impact of climate change on flow regimes and subsequent changes in wetland connectivity were quantified for different flood events. Flood inundation was simulated using a two-dimensional hydrodynamic model (MIKE 21). Five flood events ranging from 1 in 2 years flooding through to large infrequent flooding was investigated. As expected, wetland connectivity varied under the different flood scenarios with many wetlands connected with rivers for a short period of time under a small flood and others only connected during a large flood events. Wetlands located in the downstream part of the floodplain experienced a longer duration of connection compared to those located in the upper part of the floodplain. Results showed a decrease in connectivity under projected dry climate compared to an increase in connectivity under a projected wet climate. This information is critical to future studies on ecological health and biodiversity of floodplain wetlands.