Hydrological connectivity between wetlands and the main streams is a major determinant of the ecological condition of floodplain systems. This paper describes the application of MIKE 21 hydrodynamic (HD) modelling tool to assess the hydrological connectivity between floodplain wetlands and main rivers in the Flinders catchment in north Queensland, Australia. The SRTM (Shuttle Radar Topography Mission) derived 30 m DEM was used to reproduce floodplain topography and stream networks in the HD model. Land surface roughness parameters were estimated using a land use map derived from remotely sensed data. The model was calibrated using stream gauge records (stage heights) on the floodplain and inundation maps derived from a combination of MODIS imagery. An algorithm was developed to combine the HD model results with floodplain topology to quantify flood inundation and connectivity between wetlands and rivers. The connectivity of 18 off-stream wetlands, which are considered ecologically important to fish population, was quantified for 3 different floods. The impacts of climate change on connectivity to individual wetland were assessed for Cdry (dry climate), Cwet (wet climate) and SLR (sea level rise) conditions. The results reveal that connectivity will decrease under dry climate and increase under wet climate while impact of SLR is minimal. The information could be useful to future studies on movement and recruitment patterns of aquatic biota during floods.