Periodic inundation of floodplains and wetlands is critical for the well being of ecosystems. This study proposes a simple but efficient model that integrates time series daily flow data and the Landsat-derived Water Observation from Space (WOfS) product to model the spatio-temporal flood inundation dynamics of the Murray-Darling Basin. A zone-gauge framework is adopted in order to reduce the hydrologic complexity of the large river basin. Under this framework, flood frequency analysis was conducted at each gauge station to identify historical peak flows and their annual exceedance probabilities. The results were then linked with the WOfS dataset through date to model the inundation probability in each zone. Inundation frequency was derived by simply overlaying the yearly inundation extent from 1988 to 2015 and counting the inundation times. Both the resultant inundation frequency map and inundation probability map are of ecological significance for the survival and prosperity of riparian ecosystems. The assumptions of the model were validated carefully to enhance its theoretical basis. The WOfS dataset was also compared with another independent water observation dataset to cross-validate its reliability. It is hoped that with the development of more and more global high-resolution surface water datasets, this study could inspire more studies that integrate surface water datasets with hydrological observations for flood inundation modeling.