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The Chobe River, characterized by an unusual flood pulsing regime and shared between Botswana and Namibia, lies at the heart of the world’s largest transfrontier conservation area (the Kavango-Zambezi Transfrontier Conservation Area). Significant ecological changes and vegetation conversions are occurring along its floodplains. Various scenarios for agricultural and urban water use are currently being proposed by the government of Botswana. However, the understanding of the river’s annual flow regime and timing of the relative contributions of water from three different sources is relatively poor. In light of past and future climate change and variability, this means that allocating water between ecological flows and economic and domestic uses will become increasingly challenging. We reconstruct the inundation history in this basin to help ease this challenge. This paper presents a spatiotemporal approach to estimate the contribution of water from various sources and the magnitude of changes in the flooding extent in the basin between 1985 and 2010. We used time series analysis of bimonthly NOAA AVHRR and NASA MODIS data and climatologic and hydrologic records to determine the flooding timing and extent. The results indicate that between 12 and 62 % of the basin is flooded on an annual basis and that the spatial extent of the flooding varies throughout the year as a function of the timing of peak discharge in two larger basins. A 30-year trend analysis indicates a consistent decline in the average monthly flooded area in the basin. The results may prove useful in future water utilization feasibility studies, in determining measures for protecting ecological flows and levels, and in ecosystem dynamics studies in the context of current and future climate change and variability.